Variant 7-143356630-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001031690.3(FAM131B):c.1003G>A(p.Ala335Thr) variant causes a missense change. The variant allele was found at a frequency of 0.195 in 1,613,588 control chromosomes in the GnomAD database, including 32,438 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 0.18 ( 2868 hom., cov: 31)

Exomes 𝑓: 0.20 ( 29570 hom. )

Consequence

FAM131B
NM_001031690.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.98

Variant links:

Genes affected

FAM131B (HGNC:22202): (family with sequence similarity 131 member B) Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

FAM131B 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=0.0013714731).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM131B	NM_001031690.3 link	c.1003G>A	p.Ala335Thr	missense_variant	7/7	ENST00000443739.7	NP_001026860.2	Q86XD5-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM131B	ENST00000443739.7 link	c.1003G>A	p.Ala335Thr	missense_variant	7/7	1	NM_001031690.3	ENSP00000410603.2		Q86XD5-3

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28061

AN:

151748

Hom.:

2868

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.210

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.198

GnomAD3 exomes

AF:

0.214

AC:

53932

AN:

251432

Hom.:

6288

AF XY:

0.212

AC XY:

28747

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.263

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.269

Gnomad SAS exome

AF:

0.160

Gnomad FIN exome

AF:

0.276

Gnomad NFE exome

AF:

0.198

Gnomad OTH exome

AF:

0.215

GnomAD4 exome

AF:

0.196

AC:

285847

AN:

1461720

Hom.:

29570

Cov.:

AF XY:

0.195

AC XY:

141748

AN XY:

727176

show subpopulations

Gnomad4 AFR exome

AF:

0.114

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.353

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.267

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.199

GnomAD4 genome

AF:

0.185

AC:

28069

AN:

151868

Hom.:

2868

Cov.:

AF XY:

0.189

AC XY:

13997

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.286

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.277

Gnomad4 NFE

AF:

0.193

Gnomad4 OTH

AF:

0.195

Alfa

AF:

0.201

Hom.:

5097

Bravo

AF:

0.181

TwinsUK

AF:

0.186

AC:

691

ALSPAC

AF:

0.184

AC:

709

ESP6500AA

AF:

0.124

AC:

546

ESP6500EA

AF:

0.193

AC:

1662

ExAC

AF:

0.211

AC:

25567

Asia WGS

AF:

0.205

AC:

714

AN:

3478

EpiCase

AF:

0.200

EpiControl

AF:

0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.010

.;.;T;T;T

Eigen

Benign

0.080

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.84

T;T;.;.;T

MetaRNN

Benign

0.0014

T;T;T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.0

.;.;L;L;L

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-0.39

N;N;N;N;N

REVEL

Benign

0.070

Sift

Benign

0.35

T;T;T;T;T

Sift4G

Benign

0.55

T;T;T;T;T

Polyphen

0.20, 0.64

.;B;P;P;P

Vest4

0.10

MPC

0.66

ClinPred

0.0085

GERP RS

5.8

Varity_R

0.054

gMVP

0.041

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