Variant 16-48224287-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001370497.1(ABCC11):c.538G>A(p.Gly180Arg) variant causes a missense change. The variant allele was found at a frequency of 0.166 in 1,613,704 control chromosomes in the GnomAD database, including 38,952 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 3460 hom., cov: 32)

Exomes 𝑓: 0.17 ( 35492 hom. )

Consequence

ABCC11
NM_001370497.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:4

Conservation

PhyloP100: 4.13

Variant links:

Genes affected

ABCC11 (HGNC:14639): (ATP binding cassette subfamily C member 11) 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 ABC full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. The product of this gene participates in physiological processes involving bile acids, conjugated steroids, and cyclic nucleotides. In addition, a SNP in this gene is responsible for determination of human earwax type. This gene and family member ABCC12 are determined to be derived by duplication and are both localized to chromosome 16q12.1. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008]

ABCC11 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 (MetaRNN=1.0881486E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC11	NM_001370497.1 linkuse as main transcript	c.538G>A	p.Gly180Arg	missense_variant	5/30	ENST00000356608.7	NP_001357426.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC11	ENST00000356608.7 linkuse as main transcript	c.538G>A	p.Gly180Arg	missense_variant	5/30	1	NM_001370497.1	ENSP00000349017	P1	Q96J66-1

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21551

AN:

152078

Hom.:

3463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0286

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.838

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.126

GnomAD3 exomes

AF:

0.224

AC:

56232

AN:

251088

Hom.:

11923

AF XY:

0.232

AC XY:

31474

AN XY:

135698

show subpopulations

Gnomad AFR exome

AF:

0.0267

Gnomad AMR exome

AF:

0.162

Gnomad ASJ exome

AF:

0.108

Gnomad EAS exome

AF:

0.870

Gnomad SAS exome

AF:

0.406

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.129

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.168

AC:

245580

AN:

1461508

Hom.:

35492

Cov.:

AF XY:

0.175

AC XY:

127485

AN XY:

727046

show subpopulations

Gnomad4 AFR exome

AF:

0.0218

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.875

Gnomad4 SAS exome

AF:

0.404

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.174

GnomAD4 genome

AF:

0.142

AC:

21545

AN:

152196

Hom.:

3460

Cov.:

AF XY:

0.153

AC XY:

11395

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0285

Gnomad4 AMR

AF:

0.113

Gnomad4 ASJ

AF:

0.113

Gnomad4 EAS

AF:

0.839

Gnomad4 SAS

AF:

0.426

Gnomad4 FIN

AF:

0.243

Gnomad4 NFE

AF:

0.128

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.132

Hom.:

4732

Bravo

AF:

0.130

TwinsUK

AF:

0.123

AC:

456

ALSPAC

AF:

0.131

AC:

506

ESP6500AA

AF:

0.0314

AC:

138

ESP6500EA

AF:

0.132

AC:

1136

ExAC

AF:

0.225

AC:

27283

Asia WGS

AF:

0.497

AC:

1723

AN:

3478

EpiCase

AF:

0.120

EpiControl

AF:

0.119

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Apocrine gland secretion, variation in

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Feb 28, 2011

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Colostrum secretion

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Feb 28, 2011

- -

Axillary odor

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Feb 28, 2011

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.86

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Pathogenic

0.14

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.34

.;T;T;T

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.77

T;.;.;T

MetaRNN

Benign

0.000011

T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Pathogenic

2.9

M;M;M;M

MutationTaster

Benign

0.00020

P;P;P;P;P

PrimateAI

Benign

0.47

PROVEAN

Pathogenic

-6.5

D;D;D;D

REVEL

Pathogenic

0.70

Sift

Uncertain

0.0010

D;D;D;D

Sift4G

Pathogenic

0.0010

D;D;D;D

Polyphen

1.0

D;D;D;D

Vest4

0.58

MutPred

0.29

Loss of catalytic residue at V178 (P = 0.1257);Loss of catalytic residue at V178 (P = 0.1257);Loss of catalytic residue at V178 (P = 0.1257);Loss of catalytic residue at V178 (P = 0.1257);

MPC

0.53

ClinPred

0.036

GERP RS

4.5

Varity_R

0.74

gMVP

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over