chr17-50676062-C-T

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

2

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]

Genome browser will be placed here

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
ABCC3NM_003786.4 linkuse as main transcriptc.3039C>T p.Gly1013= synonymous_variant 22/31 ENST00000285238.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCC3ENST00000285238.13 linkuse as main transcriptc.3039C>T p.Gly1013= synonymous_variant 22/311 NM_003786.4 P1O15438-1

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15488
AN:
152052
Hom.:
1070
Cov.:
32
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.:
35
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.:
32
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.

Other links and lift over

dbSNP: rs4148416; hg19: chr17-48753423; API