rs1229984

chr4-99318162-T-Achr4-99318162-T-Cchr4-99318162-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_000668(ADH1B):c.143A>T(p.His48Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H48R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Consequence

ADH1B
NM_000668 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Links

ADH1B (HGNC:250):

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 31.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADH1B	NM_000668.6 linkuse as main transcript	c.143A>T	p.His48Leu	missense_variant	3/9	ENST00000305046.13
ADH1B	NM_001286650.2 linkuse as main transcript	c.23A>T	p.His8Leu	missense_variant	4/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADH1B	ENST00000305046.13 linkuse as main transcript	c.143A>T	p.His48Leu	missense_variant	3/9	1	NM_000668.6	P1	P00325-1

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.43

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.69

Cadd

Benign

Dann

Benign

0.95

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.52

FATHMM_MKL

Uncertain

0.92

M_CAP

Benign

0.0058

MetaRNN

Uncertain

0.45

T;T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.97

D;D

PrimateAI

Benign

0.26

PROVEAN

Pathogenic

-4.5

D;.;.;.

REVEL

Benign

0.10

Sift

Benign

0.037

D;.;.;.

Sift4G

Uncertain

0.0060

D;D;D;.

Vest4

0.28

MutPred

0.76

.;Loss of disorder (P = 0.005);Loss of disorder (P = 0.005);.;

MVP

0.28

MPC

0.22

ClinPred

0.88

GERP RS

3.6

gMVP

0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over