Variant chr17-50676062-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003786.4(ABCC3):c.3039C>T(p.Gly1013=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 1,614,004 control chromosomes in the GnomAD database, including 4,905 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 0.10 ( 1068 hom., cov: 32)

Exomes 𝑓: 0.065 ( 3837 hom. )

Consequence

ABCC3
NM_003786.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.29

Variant links:

Genes affected

ABCC3 (HGNC:54): (ATP binding cassette subfamily C member 3) 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 MRP subfamily which is involved in multi-drug resistance. The specific function of this protein has not yet been determined; however, this protein may play a role in the transport of biliary and intestinal excretion of organic anions. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

ABCC3 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=-0.73).

BP7

Synonymous conserved (PhyloP=-3.29 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC3	NM_003786.4 linkuse as main transcript	c.3039C>T	p.Gly1013=	synonymous_variant	22/31	ENST00000285238.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC3	ENST00000285238.13 linkuse as main transcript	c.3039C>T	p.Gly1013=	synonymous_variant	22/31	1	NM_003786.4	P1	O15438-1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15488

AN:

152052

Hom.:

1070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.0620

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.0889

Gnomad FIN

AF:

0.0496

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0546

Gnomad OTH

AF:

0.0782

GnomAD3 exomes

AF:

0.0871

AC:

21895

AN:

251378

Hom.:

1282

AF XY:

0.0816

AC XY:

11082

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.143

Gnomad ASJ exome

AF:

0.0581

Gnomad EAS exome

AF:

0.151

Gnomad SAS exome

AF:

0.0879

Gnomad FIN exome

AF:

0.0497

Gnomad NFE exome

AF:

0.0539

Gnomad OTH exome

AF:

0.0727

GnomAD4 exome

AF:

0.0646

AC:

94422

AN:

1461836

Hom.:

3837

Cov.:

AF XY:

0.0646

AC XY:

46993

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.198

Gnomad4 AMR exome

AF:

0.139

Gnomad4 ASJ exome

AF:

0.0565

Gnomad4 EAS exome

AF:

0.113

Gnomad4 SAS exome

AF:

0.0868

Gnomad4 FIN exome

AF:

0.0520

Gnomad4 NFE exome

AF:

0.0544

Gnomad4 OTH exome

AF:

0.0716

GnomAD4 genome

AF:

0.102

AC:

15496

AN:

152168

Hom.:

1068

Cov.:

AF XY:

0.102

AC XY:

7606

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.191

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.0620

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.0873

Gnomad4 FIN

AF:

0.0496

Gnomad4 NFE

AF:

0.0546

Gnomad4 OTH

AF:

0.0798

Alfa

AF:

0.0666

Hom.:

805

Bravo

AF:

0.112

Asia WGS

AF:

0.122

AC:

425

AN:

3478

EpiCase

AF:

0.0546

EpiControl

AF:

0.0554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.097

DANN

Benign

0.40

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

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