Variant rs61732039 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.1109A>G(p.Asp370Gly) variant causes a missense change. The variant allele was found at a frequency of 0.119 in 1,598,770 control chromosomes in the GnomAD database, including 12,606 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 0.097 ( 921 hom., cov: 33)

Exomes 𝑓: 0.12 ( 11685 hom. )

Consequence

ABCB5
NM_001163941.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.94

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:

ABCB5 (HGNC:):

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=0.002119571).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 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.1109A>G	p.Asp370Gly	missense_variant	11/28	ENST00000404938.7	NP_001157413.1	Q2M3G0-4
ABCB5	NM_178559.6 linkuse as main transcript	c.-227A>G		5_prime_UTR_variant	2/19		NP_848654.3	Q2M3G0-1
ABCB5	NM_001163942.2 linkuse as main transcript	c.-227A>G		5_prime_UTR_variant	2/6		NP_001157414.1	Q2M3G0-2A0A024RA03
ABCB5	NM_001163993.3 linkuse as main transcript	c.-227A>G		5_prime_UTR_variant	2/6		NP_001157465.1	Q2M3G0-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7 linkuse as main transcript	c.1109A>G	p.Asp370Gly	missense_variant	11/28	1	NM_001163941.2	ENSP00000384881.2		Q2M3G0-4

Frequencies

GnomAD3 genomes

AF:

0.0974

AC:

14819

AN:

152146

Hom.:

921

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0270

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.0931

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0573

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.0865

GnomAD3 exomes

AF:

0.103

AC:

25514

AN:

246530

Hom.:

1692

AF XY:

0.106

AC XY:

14173

AN XY:

133974

show subpopulations

Gnomad AFR exome

AF:

0.0234

Gnomad AMR exome

AF:

0.0601

Gnomad ASJ exome

AF:

0.118

Gnomad EAS exome

AF:

0.00117

Gnomad SAS exome

AF:

0.0653

Gnomad FIN exome

AF:

0.197

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.112

GnomAD4 exome

AF:

0.121

AC:

175034

AN:

1446506

Hom.:

11685

Cov.:

AF XY:

0.120

AC XY:

86476

AN XY:

720470

show subpopulations

Gnomad4 AFR exome

AF:

0.0211

Gnomad4 AMR exome

AF:

0.0624

Gnomad4 ASJ exome

AF:

0.120

Gnomad4 EAS exome

AF:

0.000808

Gnomad4 SAS exome

AF:

0.0657

Gnomad4 FIN exome

AF:

0.192

Gnomad4 NFE exome

AF:

0.132

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.0973

AC:

14820

AN:

152264

Hom.:

921

Cov.:

AF XY:

0.0986

AC XY:

7342

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0269

Gnomad4 AMR

AF:

0.0930

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0578

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.0856

Alfa

AF:

0.120

Hom.:

1335

Bravo

AF:

0.0866

TwinsUK

AF:

0.140

AC:

519

ALSPAC

AF:

0.136

AC:

526

ESP6500AA

AF:

0.0284

AC:

ESP6500EA

AF:

0.134

AC:

962

ExAC

AF:

0.103

AC:

12379

Asia WGS

AF:

0.0270

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.28

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.25

Eigen

Uncertain

0.64

Eigen_PC

Uncertain

0.56

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.79

MetaRNN

Benign

0.0021

MetaSVM

Benign

-0.82

PrimateAI

Benign

0.46

PROVEAN

Pathogenic

-5.9

REVEL

Pathogenic

0.65

Sift

Uncertain

0.0020

Sift4G

Uncertain

0.0040

Vest4

0.12

MPC

0.0095

ClinPred

0.063

GERP RS

4.2

Varity_R

0.56

gMVP

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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