Variant chr7-44977022-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_033054.3(MYO1G):c.145G>A(p.Val49Met) variant causes a missense change. The variant allele was found at a frequency of 0.203 in 1,613,356 control chromosomes in the GnomAD database, including 35,980 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.19 ( 3135 hom., cov: 33)

Exomes 𝑓: 0.20 ( 32845 hom. )

Consequence

MYO1G
NM_033054.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.01

Variant links:

Genes affected

MYO1G (HGNC:13880): (myosin IG) MYO1G is a plasma membrane-associated class I myosin (see MIM 601478) that is abundant in T and B lymphocytes and mast cells (Pierce et al., 2001 [PubMed 11544309]; Patino-Lopez et al., 2010 [PubMed 20071333]).[supplied by OMIM, Jun 2010]

MYO1G 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=0.0056494176).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO1G	NM_033054.3 linkuse as main transcript	c.145G>A	p.Val49Met	missense_variant	2/22	ENST00000258787.12	NP_149043.2
MYO1G	XR_007060129.1 linkuse as main transcript	n.199G>A		non_coding_transcript_exon_variant	2/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO1G	ENST00000258787.12 linkuse as main transcript	c.145G>A	p.Val49Met	missense_variant	2/22	1	NM_033054.3	ENSP00000258787	P1	B0I1T2-1

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29042

AN:

152098

Hom.:

3133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.0939

Gnomad SAS

AF:

0.0719

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.184

AC:

46100

AN:

249892

Hom.:

5027

AF XY:

0.182

AC XY:

24647

AN XY:

135308

show subpopulations

Gnomad AFR exome

AF:

0.146

Gnomad AMR exome

AF:

0.150

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.102

Gnomad SAS exome

AF:

0.0668

Gnomad FIN exome

AF:

0.350

Gnomad NFE exome

AF:

0.219

Gnomad OTH exome

AF:

0.199

GnomAD4 exome

AF:

0.204

AC:

298797

AN:

1461140

Hom.:

32845

Cov.:

AF XY:

0.200

AC XY:

145383

AN XY:

726880

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.153

Gnomad4 ASJ exome

AF:

0.120

Gnomad4 EAS exome

AF:

0.0750

Gnomad4 SAS exome

AF:

0.0694

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.191

AC:

29055

AN:

152216

Hom.:

3135

Cov.:

AF XY:

0.195

AC XY:

14488

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.0939

Gnomad4 SAS

AF:

0.0711

Gnomad4 FIN

AF:

0.360

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.206

Hom.:

2823

Bravo

AF:

0.179

TwinsUK

AF:

0.215

AC:

797

ALSPAC

AF:

0.227

AC:

873

ESP6500AA

AF:

0.148

AC:

652

ESP6500EA

AF:

0.213

AC:

1829

ExAC

AF:

0.182

AC:

22070

Asia WGS

AF:

0.0800

AC:

278

AN:

3478

EpiCase

AF:

0.212

EpiControl

AF:

0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.17

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.45

T;.

Eigen

Uncertain

0.43

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Benign

0.67

LIST_S2

Uncertain

0.93

D;D

MetaRNN

Benign

0.0056

T;T

MetaSVM

Benign

-1.2

MutationAssessor

Benign

1.9

L;.

MutationTaster

Benign

0.000047

PrimateAI

Uncertain

0.75

PROVEAN

Benign

-2.0

N;.

REVEL

Uncertain

0.58

Sift

Benign

0.20

T;.

Sift4G

Benign

0.20

T;.

Polyphen

0.99

D;.

Vest4

0.20

MPC

0.96

ClinPred

0.015

GERP RS

3.9

Varity_R

0.10

gMVP

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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