Variant 7-44966198-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_033054.3(MYO1G):c.2032C>A(p.His678Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,612,496 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0046 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0048 ( 26 hom. )

Consequence

MYO1G
NM_033054.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.42

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:

MYO1G (HGNC:):

MYO1G links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007805586).

BP6

Variant 7-44966198-G-T is Benign according to our data. Variant chr7-44966198-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388060.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO1G	NM_033054.3 linkuse as main transcript	c.2032C>A	p.His678Asn	missense_variant	16/22	ENST00000258787.12	NP_149043.2	B0I1T2-1
MYO1G	XR_007060129.1 linkuse as main transcript	n.2086C>A		non_coding_transcript_exon_variant	16/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO1G	ENST00000258787.12 linkuse as main transcript	c.2032C>A	p.His678Asn	missense_variant	16/22	1	NM_033054.3	ENSP00000258787.7		B0I1T2-1

Frequencies

GnomAD3 genomes

AF:

0.00456

AC:

693

AN:

152026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000626

Gnomad FIN

AF:

0.0168

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00654

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00430

AC:

1069

AN:

248538

Hom.:

AF XY:

0.00422

AC XY:

569

AN XY:

134832

show subpopulations

Gnomad AFR exome

AF:

0.000935

Gnomad AMR exome

AF:

0.000899

Gnomad ASJ exome

AF:

0.00140

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000458

Gnomad FIN exome

AF:

0.0150

Gnomad NFE exome

AF:

0.00592

Gnomad OTH exome

AF:

0.00361

GnomAD4 exome

AF:

0.00484

AC:

7064

AN:

1460352

Hom.:

Cov.:

AF XY:

0.00478

AC XY:

3470

AN XY:

726506

show subpopulations

Gnomad4 AFR exome

AF:

0.000627

Gnomad4 AMR exome

AF:

0.000895

Gnomad4 ASJ exome

AF:

0.00207

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000360

Gnomad4 FIN exome

AF:

0.0140

Gnomad4 NFE exome

AF:

0.00539

Gnomad4 OTH exome

AF:

0.00325

GnomAD4 genome

AF:

0.00455

AC:

693

AN:

152144

Hom.:

Cov.:

AF XY:

0.00471

AC XY:

350

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.000746

Gnomad4 AMR

AF:

0.00118

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000627

Gnomad4 FIN

AF:

0.0168

Gnomad4 NFE

AF:

0.00654

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00504

Hom.:

Bravo

AF:

0.00299

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00623

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00616

AC:

ExAC

AF:

0.00418

AC:

507

EpiCase

AF:

0.00442

EpiControl

AF:

0.00551

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

MYO1G: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.18

T;.

Eigen

Benign

-0.11

Eigen_PC

Benign

0.050

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.62

T;T

MetaRNN

Benign

0.0078

T;T

MetaSVM

Benign

-0.86

MutationAssessor

Benign

0.86

L;.

PrimateAI

Uncertain

0.70

PROVEAN

Benign

-1.7

N;.

REVEL

Benign

0.074

Sift

Benign

0.31

T;.

Sift4G

Benign

0.31

T;.

Polyphen

0.060

B;.

Vest4

0.57

MVP

0.64

MPC

0.73

ClinPred

0.013

GERP RS

4.5

Varity_R

0.25

gMVP

0.70

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over