Variant 7-20643261-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001163941.2(ABCB5):c.392C>T(p.Thr131Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0338 in 1,613,684 control chromosomes in the GnomAD database, including 1,312 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 0.041 ( 199 hom., cov: 33)

Exomes 𝑓: 0.033 ( 1113 hom. )

Consequence

ABCB5
NM_001163941.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.82

Variant links:

Genes affected

ABCB5 (HGNC:46): (ATP binding cassette subfamily B member 5) ABCB5 belongs to the ATP-binding cassette (ABC) transporter superfamily of integral membrane proteins. These proteins participate in ATP-dependent transmembrane transport of structurally diverse molecules ranging from small ions, sugars, and peptides to more complex organic molecules (Chen et al., 2005 [PubMed 15760339]).[supplied by OMIM, Mar 2008]

ABCB5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCB5	NM_001163941.2 linkuse as main transcript	c.392C>T	p.Thr131Ile	missense_variant	6/28	ENST00000404938.7	NP_001157413.1	Q2M3G0-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7 linkuse as main transcript	c.392C>T	p.Thr131Ile	missense_variant	6/28	1	NM_001163941.2	ENSP00000384881.2		Q2M3G0-4

Frequencies

GnomAD3 genomes

AF:

0.0415

AC:

6313

AN:

152144

Hom.:

199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0678

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0201

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.108

Gnomad SAS

AF:

0.0911

Gnomad FIN

AF:

0.0188

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0275

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.0390

AC:

9678

AN:

248226

Hom.:

321

AF XY:

0.0409

AC XY:

5516

AN XY:

134868

show subpopulations

Gnomad AFR exome

AF:

0.0715

Gnomad AMR exome

AF:

0.00971

Gnomad ASJ exome

AF:

0.0122

Gnomad EAS exome

AF:

0.111

Gnomad SAS exome

AF:

0.0796

Gnomad FIN exome

AF:

0.0167

Gnomad NFE exome

AF:

0.0283

Gnomad OTH exome

AF:

0.0273

GnomAD4 exome

AF:

0.0330

AC:

48217

AN:

1461422

Hom.:

1113

Cov.:

AF XY:

0.0344

AC XY:

24976

AN XY:

726944

show subpopulations

Gnomad4 AFR exome

AF:

0.0764

Gnomad4 AMR exome

AF:

0.0101

Gnomad4 ASJ exome

AF:

0.0115

Gnomad4 EAS exome

AF:

0.0930

Gnomad4 SAS exome

AF:

0.0785

Gnomad4 FIN exome

AF:

0.0182

Gnomad4 NFE exome

AF:

0.0281

Gnomad4 OTH exome

AF:

0.0331

GnomAD4 genome

AF:

0.0415

AC:

6317

AN:

152262

Hom.:

199

Cov.:

AF XY:

0.0421

AC XY:

3135

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0678

Gnomad4 AMR

AF:

0.0201

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.108

Gnomad4 SAS

AF:

0.0906

Gnomad4 FIN

AF:

0.0188

Gnomad4 NFE

AF:

0.0274

Gnomad4 OTH

AF:

0.0241

Alfa

AF:

0.0292

Hom.:

117

Bravo

AF:

0.0409

TwinsUK

AF:

0.0299

AC:

111

ALSPAC

AF:

0.0267

AC:

103

ESP6500AA

AF:

0.0727

AC:

228

ESP6500EA

AF:

0.0274

AC:

196

ExAC

AF:

0.0416

AC:

5012

EpiCase

AF:

0.0269

EpiControl

AF:

0.0265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.51

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.18

Eigen

Benign

-0.026

Eigen_PC

Benign

-0.14

FATHMM_MKL

Benign

0.54

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.0032

MetaSVM

Benign

-0.94

PrimateAI

Benign

0.42

PROVEAN

Benign

-1.8

REVEL

Uncertain

0.34

Sift

Uncertain

0.0010

Sift4G

Benign

0.081

Vest4

0.10

MPC

0.020

ClinPred

0.048

GERP RS

3.0

Varity_R

0.24

gMVP

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.25

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.25

Position offset: 6

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