Genetic Variant NM_000350.3:c.2828G>A (chr1-94047009-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 5P and 13B. PM1PM5PP2BP4_StrongBP6BS1BS2

The NM_000350.3(ABCA4):c.2828G>A(p.Arg943Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 1,614,062 control chromosomes in the GnomAD database, including 1,540 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R943G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.029 ( 98 hom., cov: 32)

Exomes 𝑓: 0.042 ( 1442 hom. )

Consequence

ABCA4
NM_000350.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3U:2B:17O:2

Conservation

PhyloP100: 1.07

Publications

41 publications found

Variant links:

Genes affected

ABCA4 (HGNC:34): (ATP binding cassette subfamily A member 4) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]

ABCA4 Gene-Disease associations (from GenCC):

ABCA4-related retinopathy
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
cone-rod dystrophy 3
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
severe early-childhood-onset retinal dystrophy
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Ambry Genetics
retinitis pigmentosa 19
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
cone-rod dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
retinitis pigmentosa
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Stargardt disease
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
age related macular degeneration 2
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ABCA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

PM1

In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 13 uncertain in NM_000350.3

PM5

Other missense variant is known to change same aminoacid residue: Variant chr1-94047010-G-A is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 99162.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

PP2

Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 578 curated pathogenic missense variants (we use a threshold of 10). The gene has 28 curated benign missense variants. Gene score misZ: -0.65813 (below the threshold of 3.09). Trascript score misZ: 1.3628 (below the threshold of 3.09). GenCC associations: The gene is linked to severe early-childhood-onset retinal dystrophy, retinitis pigmentosa, age related macular degeneration 2, retinitis pigmentosa 19, cone-rod dystrophy 3, ABCA4-related retinopathy, Stargardt disease, cone-rod dystrophy.

BP4

Computational evidence support a benign effect (MetaRNN=0.0059529543).

BP6

Variant 1-94047009-C-T is Benign according to our data. Variant chr1-94047009-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 7913.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0291 (4430/152184) while in subpopulation NFE AF = 0.0433 (2942/68002). AF 95% confidence interval is 0.042. There are 98 homozygotes in GnomAd4. There are 2120 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 98 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000350.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA4	NM_000350.3	MANE Select	c.2828G>A	p.Arg943Gln	missense	Exon 19 of 50	NP_000341.2	P78363
	ABCA4	NM_001425324.1		c.2606G>A	p.Arg869Gln	missense	Exon 18 of 49	NP_001412253.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA4	ENST00000370225.4	TSL:1 MANE Select	c.2828G>A	p.Arg943Gln	missense	Exon 19 of 50	ENSP00000359245.3	P78363
	ABCA4	ENST00000649773.1		c.2606G>A	p.Arg869Gln	missense	Exon 18 of 19	ENSP00000496882.1	A0A3B3IRV8

Frequencies

GnomAD3 genomes

AF:

0.0291

AC:

4428

AN:

152066

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0422

Gnomad FIN

AF:

0.0298

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0433

Gnomad OTH

AF:

0.0301

GnomAD2 exomes

AF:

0.0302

AC:

7592

AN:

251410

AF XY:

0.0322

show subpopulations

Gnomad AFR exome

AF:

0.0104

Gnomad AMR exome

AF:

0.0117

Gnomad ASJ exome

AF:

0.0212

Gnomad EAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.0317

Gnomad NFE exome

AF:

0.0408

Gnomad OTH exome

AF:

0.0314

GnomAD4 exome

AF:

0.0418

AC:

61092

AN:

1461878

Hom.:

1442

Cov.:

AF XY:

0.0416

AC XY:

30260

AN XY:

727244

show subpopulations

African (AFR)

AF:

0.0109

AC:

366

AN:

33480

American (AMR)

AF:

0.0121

AC:

543

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0200

AC:

522

AN:

26136

East Asian (EAS)

AF:

0.000227

AC:

AN:

39700

South Asian (SAS)

AF:

0.0419

AC:

3615

AN:

86256

European-Finnish (FIN)

AF:

0.0338

AC:

1804

AN:

53420

Middle Eastern (MID)

AF:

0.0257

AC:

148

AN:

5768

European-Non Finnish (NFE)

AF:

0.0466

AC:

51866

AN:

1111998

Other (OTH)

AF:

0.0367

AC:

2219

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

3559

7117

10676

14234

17793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1962

3924

5886

7848

9810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0291

AC:

4430

AN:

152184

Hom.:

Cov.:

AF XY:

0.0285

AC XY:

2120

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0118

AC:

492

AN:

41524

American (AMR)

AF:

0.0202

AC:

309

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0202

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5168

South Asian (SAS)

AF:

0.0426

AC:

205

AN:

4808

European-Finnish (FIN)

AF:

0.0298

AC:

316

AN:

10600

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0433

AC:

2942

AN:

68002

Other (OTH)

AF:

0.0298

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

213

425

638

850

1063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

168

224

280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0363

Hom.:

419

Bravo

AF:

0.0269

TwinsUK

AF:

0.0464

AC:

172

ALSPAC

AF:

0.0439

AC:

169

ESP6500AA

AF:

0.0143

AC:

ESP6500EA

AF:

0.0410

AC:

353

ExAC

AF:

0.0307

AC:

3724

Asia WGS

AF:

0.0260

AC:

AN:

3478

EpiCase

AF:

0.0405

EpiControl

AF:

0.0421

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (6)

not provided (4)

Retinal dystrophy (2)

ABCA4-related disorder (1)

ABCA4-related retinopathy (1)

Age related macular degeneration 2 (1)

Cone-Rod Dystrophy, Recessive (1)

Macular degeneration (1)

Retinitis Pigmentosa, Recessive (1)

Severe early-childhood-onset retinal dystrophy (2)

Stargardt disease (1)

Stargardt disease 3 (1)

Stargardt Disease, Recessive (1)

MACULAR DEGENERATION, AGE-RELATED, 2, SUSCEPTIBILITY TO (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.14

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.38

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.17

FATHMM_MKL

Benign

0.51

LIST_S2

Benign

0.84

MetaRNN

Benign

0.0060

MetaSVM

Benign

-0.48

MutationAssessor

Benign

1.3

PhyloP100

1.1

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.0

REVEL

Uncertain

0.35

Sift

Benign

0.29

Sift4G

Benign

0.15

Polyphen

0.010

Vest4

0.15

MPC

0.18

ClinPred

0.0089

GERP RS

3.5

Varity_R

0.075

gMVP

0.75

Mutation Taster

=94/6

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over