Genetic Variant NM_001137560.2:c.283G>T (chr6-44273213-G-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001137560.2(TMEM151B):c.283G>T(p.Ala95Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000093 in 1,398,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000093 ( 0 hom. )

Consequence

TMEM151B
NM_001137560.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.90

Variant links:

Genes affected

TMEM151B (HGNC:21315): (transmembrane protein 151B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM151B links:

ENSG00000272442 (HGNC:):

ENSG00000272442 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.14622328).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM151B	NM_001137560.2 link	c.283G>T	p.Ala95Ser	missense_variant	Exon 2 of 3	ENST00000451188.7	NP_001131032.1	Q8IW70-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TMEM151B	ENST00000451188.7 link	c.283G>T	p.Ala95Ser	missense_variant	Exon 2 of 3	5	NM_001137560.2	ENSP00000393161.2	Q8IW70-1
ENSG00000272442	ENST00000505802.1 link	n.19G>T		non_coding_transcript_exon_variant	Exon 1 of 10	2		ENSP00000424257.1	H0Y9J4
TMEM151B	ENST00000438774.2 link	c.283G>T	p.Ala95Ser	missense_variant	Exon 2 of 3	3		ENSP00000409337.2	Q8IW70-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000930

AC:

AN:

1398000

Hom.:

Cov.:

AF XY:

0.00000580

AC XY:

AN XY:

689228

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000121

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Uncertain

0.016

BayesDel_noAF

Benign

-0.21

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0083

T;.

Eigen

Benign

0.067

Eigen_PC

Benign

0.18

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.78

T;T

M_CAP

Benign

0.0043

MetaRNN

Benign

0.15

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.3

L;L

PrimateAI

Uncertain

0.62

PROVEAN

Benign

-0.37

N;N

REVEL

Benign

0.19

Sift

Benign

0.45

T;T

Sift4G

Benign

0.40

T;T

Polyphen

0.54

P;D

Vest4

0.32

MutPred

0.51

Gain of disorder (P = 0.0084);Gain of disorder (P = 0.0084);

MVP

0.072

ClinPred

0.73

GERP RS

4.1

Varity_R

0.11

gMVP

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over