dbSNP rs11077858: ABCA9:c.*481C>G (chr17-68975434-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080283.4(ABCA9):c.*481C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,464 control chromosomes in the GnomAD database, including 21,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 21687 hom., cov: 32)

Exomes 𝑓: 0.71 ( 133 hom. )

Consequence

ABCA9
NM_080283.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.446

Publications

11 publications found

Variant links:

Genes affected

ABCA9 (HGNC:39): (ATP binding cassette subfamily A member 9) This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two transmembrane domains and two nucleotide binding folds. 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, and White). This gene is a member of the ABC1 subfamily and is clustered with four other ABC1 family members on chromosome 17q24. Transcriptional expression of this gene is induced during monocyte differentiation into macrophages and is suppressed by cholesterol import. [provided by RefSeq, Jul 2008]

ABCA9 links:

ABCA9-AS1 (HGNC:39983): (ABCA9 antisense RNA 1)

ABCA9-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA9	NM_080283.4 link	c.*481C>G		3_prime_UTR_variant	Exon 39 of 39	ENST00000340001.9	NP_525022.2	Q8IUA7-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ABCA9	ENST00000340001.9 link	c.*481C>G	3_prime_UTR_variant	Exon 39 of 39	1	NM_080283.4	ENSP00000342216.3	Q8IUA7-1
ABCA9	ENST00000453985.6 link	c.*481C>G	3_prime_UTR_variant	Exon 38 of 38	5		ENSP00000394264.2	H0Y4U7
ABCA9-AS1	ENST00000630625.1 link	n.377+30527G>C	intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.490

AC:

74479

AN:

151858

Hom.:

21691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.741

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.627

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.580

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.605

Gnomad NFE

AF:

0.650

Gnomad OTH

AF:

0.498

GnomAD4 exome

AF:

0.711

AC:

347

AN:

488

Hom.:

133

Cov.:

AF XY:

0.679

AC XY:

159

AN XY:

234

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.671

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.763

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.713

AC:

248

AN:

348

Other (OTH)

AF:

0.929

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.490

AC:

74484

AN:

151976

Hom.:

21687

Cov.:

AF XY:

0.491

AC XY:

36456

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.164

AC:

6778

AN:

41434

American (AMR)

AF:

0.544

AC:

8305

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.627

AC:

2174

AN:

3470

East Asian (EAS)

AF:

0.330

AC:

1706

AN:

5168

South Asian (SAS)

AF:

0.580

AC:

2792

AN:

4812

European-Finnish (FIN)

AF:

0.631

AC:

6665

AN:

10560

Middle Eastern (MID)

AF:

0.606

AC:

177

AN:

292

European-Non Finnish (NFE)

AF:

0.650

AC:

44160

AN:

67960

Other (OTH)

AF:

0.497

AC:

1051

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1600

3199

4799

6398

7998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.571

Hom.:

3370

Bravo

AF:

0.465

Asia WGS

AF:

0.452

AC:

1573

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.7

(source)

DANN

Benign

0.87

PhyloP100

-0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over