Genetic Variant ABCA7:c.-9A>G (chr19-1041353-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_019112.4(ABCA7):c.-9A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 1,613,820 control chromosomes in the GnomAD database, including 5,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.048 ( 503 hom., cov: 32)

Exomes 𝑓: 0.059 ( 4950 hom. )

Consequence

ABCA7
NM_019112.4 5_prime_UTR

Scores

Splicing: ADA: 0.00002728

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0150

Variant links:

Genes affected

ABCA7 (HGNC:37): (ATP binding cassette subfamily A member 7) The 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 intra-cellular 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 full transporter has been detected predominantly in myelo-lymphatic tissues with the highest expression in peripheral leukocytes, thymus, spleen, and bone marrow. The function of this protein is not yet known; however, the expression pattern suggests a role in lipid homeostasis in cells of the immune system. [provided by RefSeq, Jul 2008]

ABCA7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-1041353-A-G is Benign according to our data. Variant chr19-1041353-A-G is described in ClinVar as [Benign]. Clinvar id is 3060463.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA7	NM_019112.4 link	c.-9A>G		5_prime_UTR_variant	Exon 2 of 47	ENST00000263094.11	NP_061985.2	Q8IZY2-1B3KUJ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA7	ENST00000263094 link	c.-9A>G		5_prime_UTR_variant	Exon 2 of 47	5	NM_019112.4	ENSP00000263094.6		Q8IZY2-1

Frequencies

GnomAD3 genomes

AF:

0.0482

AC:

7333

AN:

152116

Hom.:

493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0102

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.0441

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.0282

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0461

Gnomad OTH

AF:

0.0559

GnomAD3 exomes

AF:

0.0700

AC:

17579

AN:

251238

Hom.:

1595

AF XY:

0.0715

AC XY:

9716

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.00904

Gnomad AMR exome

AF:

0.0224

Gnomad ASJ exome

AF:

0.0540

Gnomad EAS exome

AF:

0.369

Gnomad SAS exome

AF:

0.107

Gnomad FIN exome

AF:

0.0238

Gnomad NFE exome

AF:

0.0456

Gnomad OTH exome

AF:

0.0564

GnomAD4 exome

AF:

0.0586

AC:

85706

AN:

1461586

Hom.:

4950

Cov.:

AF XY:

0.0598

AC XY:

43506

AN XY:

727074

show subpopulations

Gnomad4 AFR exome

AF:

0.00774

Gnomad4 AMR exome

AF:

0.0237

Gnomad4 ASJ exome

AF:

0.0522

Gnomad4 EAS exome

AF:

0.374

Gnomad4 SAS exome

AF:

0.105

Gnomad4 FIN exome

AF:

0.0260

Gnomad4 NFE exome

AF:

0.0482

Gnomad4 OTH exome

AF:

0.0646

GnomAD4 genome

AF:

0.0483

AC:

7354

AN:

152234

Hom.:

503

Cov.:

AF XY:

0.0507

AC XY:

3771

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0101

Gnomad4 AMR

AF:

0.0442

Gnomad4 ASJ

AF:

0.0487

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.126

Gnomad4 FIN

AF:

0.0282

Gnomad4 NFE

AF:

0.0461

Gnomad4 OTH

AF:

0.0653

Alfa

AF:

0.0463

Hom.:

322

Bravo

AF:

0.0472

Asia WGS

AF:

0.226

AC:

785

AN:

3478

EpiCase

AF:

0.0456

EpiControl

AF:

0.0477

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ABCA7-related disorder

Benign:1

Mar 29, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000027

dbscSNV1_RF

Benign

0.0

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over