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GeneBe

rs1229984

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

1
4
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Links

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
ADH1BNM_000668.6 linkuse as main transcriptc.143A>T p.His48Leu missense_variant 3/9 ENST00000305046.13
ADH1BNM_001286650.2 linkuse as main transcriptc.23A>T p.His8Leu missense_variant 4/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADH1BENST00000305046.13 linkuse as main transcriptc.143A>T p.His48Leu missense_variant 3/91 NM_000668.6 P1P00325-1

Frequencies

GnomAD3 genomes
Cov.:
31

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
T
BayesDel_noAF
Benign
-0.69
Cadd
Benign
17
Dann
Benign
0.95
Eigen
Benign
-0.60
Eigen_PC
Benign
-0.52
FATHMM_MKL
Uncertain
0.92
D
M_CAP
Benign
0.0058
T
MetaRNN
Uncertain
0.45
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
0.97
D;D
PrimateAI
Benign
0.26
T
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
D
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.

Other links and lift over

hg19: chr4-100239319;