rs35592

Variant summary

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

The NM_004996.4(ABCC1):​c.1219-176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,728 control chromosomes in the GnomAD database, including 9,145 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 0.33 ( 9145 hom., cov: 32)

Consequence

ABCC1
NM_004996.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.95
Variant links:
Genes affected
ABCC1 (HGNC:51): (ATP binding cassette subfamily C member 1 (ABCC1 blood group)) 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 full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. This protein functions as a multispecific organic anion transporter, with oxidized glutatione, cysteinyl leukotrienes, and activated aflatoxin B1 as substrates. This protein also transports glucuronides and sulfate conjugates of steroid hormones and bile salts. Alternatively spliced variants of this gene have been described but their full-length nature is unknown. [provided by RefSeq, Apr 2012]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABCC1NM_004996.4 linkuse as main transcriptc.1219-176T>C intron_variant ENST00000399410.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCC1ENST00000399410.8 linkuse as main transcriptc.1219-176T>C intron_variant 1 NM_004996.4 P1P33527-1

Frequencies

GnomAD3 genomes
AF:
0.328
AC:
49684
AN:
151610
Hom.:
9138
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.504
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.268
Gnomad EAS
AF:
0.429
Gnomad SAS
AF:
0.185
Gnomad FIN
AF:
0.304
Gnomad MID
AF:
0.232
Gnomad NFE
AF:
0.239
Gnomad OTH
AF:
0.298
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.328
AC:
49737
AN:
151728
Hom.:
9145
Cov.:
32
AF XY:
0.329
AC XY:
24389
AN XY:
74160
show subpopulations
Gnomad4 AFR
AF:
0.504
Gnomad4 AMR
AF:
0.287
Gnomad4 ASJ
AF:
0.268
Gnomad4 EAS
AF:
0.429
Gnomad4 SAS
AF:
0.185
Gnomad4 FIN
AF:
0.304
Gnomad4 NFE
AF:
0.239
Gnomad4 OTH
AF:
0.296
Alfa
AF:
0.306
Hom.:
2043
Bravo
AF:
0.340
Asia WGS
AF:
0.313
AC:
1089
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.14
DANN
Benign
0.59

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: rs35592; hg19: chr16-16141823; API