Variant rs4147912 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019112.4(ABCA7):c.2380+8A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 1,535,590 control chromosomes in the GnomAD database, including 447,163 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.79 ( 47092 hom., cov: 28)

Exomes 𝑓: 0.76 ( 400071 hom. )

Consequence

ABCA7
NM_019112.4 splice_region, intron

Scores

Splicing: ADA: 0.00003073

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.241

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA7	NM_019112.4 linkuse as main transcript	c.2380+8A>C		splice_region_variant, intron_variant		ENST00000263094.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA7	ENST00000263094.11 linkuse as main transcript	c.2380+8A>C		splice_region_variant, intron_variant		5	NM_019112.4	P1	Q8IZY2-1
ABCA7	ENST00000433129.6 linkuse as main transcript	n.3060+8A>C		splice_region_variant, intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.785

AC:

119091

AN:

151644

Hom.:

47045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.833

Gnomad AMI

AF:

0.755

Gnomad AMR

AF:

0.844

Gnomad ASJ

AF:

0.827

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.864

Gnomad FIN

AF:

0.738

Gnomad MID

AF:

0.864

Gnomad NFE

AF:

0.740

Gnomad OTH

AF:

0.796

GnomAD3 exomes

AF:

0.796

AC:

158554

AN:

199228

Hom.:

63359

AF XY:

0.795

AC XY:

86640

AN XY:

109028

show subpopulations

Gnomad AFR exome

AF:

0.836

Gnomad AMR exome

AF:

0.896

Gnomad ASJ exome

AF:

0.830

Gnomad EAS exome

AF:

0.819

Gnomad SAS exome

AF:

0.864

Gnomad FIN exome

AF:

0.732

Gnomad NFE exome

AF:

0.748

Gnomad OTH exome

AF:

0.793

GnomAD4 exome

AF:

0.759

AC:

1049982

AN:

1383828

Hom.:

400071

Cov.:

AF XY:

0.762

AC XY:

523708

AN XY:

686834

show subpopulations

Gnomad4 AFR exome

AF:

0.833

Gnomad4 AMR exome

AF:

0.885

Gnomad4 ASJ exome

AF:

0.830

Gnomad4 EAS exome

AF:

0.838

Gnomad4 SAS exome

AF:

0.863

Gnomad4 FIN exome

AF:

0.734

Gnomad4 NFE exome

AF:

0.740

Gnomad4 OTH exome

AF:

0.769

GnomAD4 genome

AF:

0.785

AC:

119189

AN:

151762

Hom.:

47092

Cov.:

AF XY:

0.787

AC XY:

58381

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.833

Gnomad4 AMR

AF:

0.844

Gnomad4 ASJ

AF:

0.827

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.862

Gnomad4 FIN

AF:

0.738

Gnomad4 NFE

AF:

0.740

Gnomad4 OTH

AF:

0.797

Alfa

AF:

0.765

Hom.:

24071

Bravo

AF:

0.795

Asia WGS

AF:

0.839

AC:

2919

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.96

DANN

Benign

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000031

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over