Variant chr7-20645861-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001163941.2(ABCB5):c.784C>A(p.Gln262Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,613,588 control chromosomes in the GnomAD database, including 7,768 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 0.044 ( 838 hom., cov: 33)

Exomes 𝑓: 0.033 ( 6930 hom. )

Consequence

ABCB5
NM_001163941.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.91

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004671544).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB5	NM_001163941.2 linkuse as main transcript	c.784C>A	p.Gln262Lys	missense_variant	8/28	ENST00000404938.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB5	ENST00000404938.7 linkuse as main transcript	c.784C>A	p.Gln262Lys	missense_variant	8/28	1	NM_001163941.2	P1	Q2M3G0-4

Frequencies

GnomAD3 genomes

AF:

0.0438

AC:

6665

AN:

152112

Hom.:

834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00707

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0893

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00488

Gnomad OTH

AF:

0.0458

GnomAD3 exomes

AF:

0.0927

AC:

23032

AN:

248356

Hom.:

3588

AF XY:

0.0836

AC XY:

11286

AN XY:

134958

show subpopulations

Gnomad AFR exome

AF:

0.00603

Gnomad AMR exome

AF:

0.243

Gnomad ASJ exome

AF:

0.0264

Gnomad EAS exome

AF:

0.487

Gnomad SAS exome

AF:

0.0884

Gnomad FIN exome

AF:

0.0870

Gnomad NFE exome

AF:

0.00534

Gnomad OTH exome

AF:

0.0629

GnomAD4 exome

AF:

0.0328

AC:

48003

AN:

1461358

Hom.:

6930

Cov.:

AF XY:

0.0332

AC XY:

24168

AN XY:

726936

show subpopulations

Gnomad4 AFR exome

AF:

0.00427

Gnomad4 AMR exome

AF:

0.234

Gnomad4 ASJ exome

AF:

0.0268

Gnomad4 EAS exome

AF:

0.480

Gnomad4 SAS exome

AF:

0.0877

Gnomad4 FIN exome

AF:

0.0820

Gnomad4 NFE exome

AF:

0.00274

Gnomad4 OTH exome

AF:

0.0440

GnomAD4 genome

AF:

0.0439

AC:

6683

AN:

152230

Hom.:

838

Cov.:

AF XY:

0.0529

AC XY:

3935

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00705

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.113

Gnomad4 FIN

AF:

0.0893

Gnomad4 NFE

AF:

0.00488

Gnomad4 OTH

AF:

0.0463

Alfa

AF:

0.0265

Hom.:

1360

Bravo

AF:

0.0511

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00337

AC:

ESP6500AA

AF:

0.00638

AC:

ESP6500EA

AF:

0.00642

AC:

ExAC

AF:

0.0831

AC:

10003

Asia WGS

AF:

0.238

AC:

824

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.27

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.090

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.37

Eigen

Pathogenic

0.73

Eigen_PC

Uncertain

0.66

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.96

MetaRNN

Benign

0.0047

MetaSVM

Benign

-1.3

MutationTaster

Benign

0.039

PrimateAI

Benign

0.41

PROVEAN

Uncertain

-3.1

REVEL

Uncertain

0.64

Sift

Uncertain

0.0020

Sift4G

Uncertain

0.0060

Vest4

0.16

MPC

0.029

ClinPred

0.028

GERP RS

4.8

Varity_R

0.81

gMVP

0.57

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.

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