Variant rs45480693 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001198934.2(ABCC10):c.782G>A(p.Arg261His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00489 in 1,614,160 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0034 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0051 ( 24 hom. )

Consequence

ABCC10
NM_001198934.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Variant links:

Genes affected

ABCC10 (HGNC:52): (ATP binding cassette subfamily C member 10) 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, and White). This ABC full-transporter is a member of the MRP subfamily which is involved in multi-drug resistance. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2010]

ABCC10 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004207194).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC10	NM_001198934.2 linkuse as main transcript	c.782G>A	p.Arg261His	missense_variant	3/22	ENST00000372530.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC10	ENST00000372530.9 linkuse as main transcript	c.782G>A	p.Arg261His	missense_variant	3/22	2	NM_001198934.2	P2	Q5T3U5-1
ABCC10	ENST00000244533.7 linkuse as main transcript	c.653G>A	p.Arg218His	missense_variant	1/20	1		A2	Q5T3U5-2
ABCC10	ENST00000372515.8 linkuse as main transcript	c.-78-473G>A		intron_variant		5
ABCC10	ENST00000443426.2 linkuse as main transcript	n.113-473G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00337

AC:

513

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00113

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00307

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00588

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00346

AC:

867

AN:

250578

Hom.:

AF XY:

0.00342

AC XY:

463

AN XY:

135548

show subpopulations

Gnomad AFR exome

AF:

0.00118

Gnomad AMR exome

AF:

0.00330

Gnomad ASJ exome

AF:

0.00417

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000980

Gnomad FIN exome

AF:

0.000278

Gnomad NFE exome

AF:

0.00584

Gnomad OTH exome

AF:

0.00376

GnomAD4 exome

AF:

0.00505

AC:

7383

AN:

1461818

Hom.:

Cov.:

AF XY:

0.00492

AC XY:

3576

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.00119

Gnomad4 AMR exome

AF:

0.00353

Gnomad4 ASJ exome

AF:

0.00394

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.0000927

Gnomad4 FIN exome

AF:

0.000525

Gnomad4 NFE exome

AF:

0.00609

Gnomad4 OTH exome

AF:

0.00404

GnomAD4 genome

AF:

0.00337

AC:

513

AN:

152342

Hom.:

Cov.:

AF XY:

0.00307

AC XY:

229

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.00307

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00588

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00529

Hom.:

Bravo

AF:

0.00387

TwinsUK

AF:

0.00297

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00535

AC:

ExAC

AF:

0.00344

AC:

417

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00660

EpiControl

AF:

0.00611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.23

Cadd

Benign

Dann

Benign

0.96

DEOGEN2

Benign

0.043

T;.

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.40

FATHMM_MKL

Benign

0.046

LIST_S2

Benign

0.71

T;T

M_CAP

Benign

0.054

MetaRNN

Benign

0.0042

T;T

MetaSVM

Benign

-0.72

MutationAssessor

Benign

1.5

L;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.62

N;N

REVEL

Benign

0.26

Sift

Benign

0.26

T;T

Sift4G

Benign

0.24

T;T

Polyphen

0.91

P;B

Vest4

0.22

MVP

0.76

MPC

0.20

ClinPred

0.0016

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.034

gMVP

0.21

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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