7-44964464-T-C

Variant names:

• chr7-44964464-T-C
• rs7792760
• NM_033054.3:c.2582A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033054.3(MYO1G):​c.2582A>G​(p.Gln861Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 1,613,836 control chromosomes in the GnomAD database, including 592,678 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 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: 𝑓 0.88 (59366 hom., cov: 32)
  • Exomes 𝑓: 0.85 (533312 hom.)
• Consequence: MYO1G NM_033054.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 28 publications found

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]

ENSG00000308366 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.0041704E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033054.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1G	NM_033054.3	MANE Select	c.2582A>G	p.Gln861Arg	missense	Exon 19 of 22	NP_149043.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1G	ENST00000258787.12	TSL:1 MANE Select	c.2582A>G	p.Gln861Arg	missense	Exon 19 of 22	ENSP00000258787.7
	MYO1G	ENST00000495831.5	TSL:1	n.*2244A>G		non_coding_transcript_exon	Exon 18 of 21	ENSP00000417650.1
	MYO1G	ENST00000495831.5	TSL:1	n.*2244A>G		3_prime_UTR	Exon 18 of 21	ENSP00000417650.1

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134031 AN: 152082 Hom.: 59311 Cov.: 32

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.848

GnomAD2 exomes AF: 0.868 AC: 218274 AN: 251414 AF XY: 0.863

Gnomad AFR exome AF: 0.969

Gnomad AMR exome AF: 0.897

Gnomad ASJ exome AF: 0.820

Gnomad EAS exome AF: 0.908

Gnomad FIN exome AF: 0.883

Gnomad NFE exome AF: 0.842

Gnomad OTH exome AF: 0.853

GnomAD4 exome AF: 0.854 AC: 1247617 AN: 1461636 Hom.: 533312 Cov.: 56 AF XY: 0.853 AC XY: 619973 AN XY: 727110

African (AFR) AF: 0.970 AC: 32461 AN: 33480

American (AMR) AF: 0.894 AC: 40000 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 21428 AN: 26136

East Asian (EAS) AF: 0.922 AC: 36593 AN: 39700

South Asian (SAS) AF: 0.863 AC: 74470 AN: 86254

European-Finnish (FIN) AF: 0.882 AC: 47027 AN: 53318

Middle Eastern (MID) AF: 0.827 AC: 4766 AN: 5764

European-Non Finnish (NFE) AF: 0.845 AC: 939164 AN: 1111876

Other (OTH) AF: 0.856 AC: 51708 AN: 60384

GnomAD4 genome AF: 0.881 AC: 134145 AN: 152200 Hom.: 59366 Cov.: 32 AF XY: 0.882 AC XY: 65638 AN XY: 74416

African (AFR) AF: 0.966 AC: 40119 AN: 41528

American (AMR) AF: 0.848 AC: 12974 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4703 AN: 5166

South Asian (SAS) AF: 0.860 AC: 4152 AN: 4826

European-Finnish (FIN) AF: 0.883 AC: 9359 AN: 10598

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57131 AN: 67998

Other (OTH) AF: 0.848 AC: 1791 AN: 2112

Alfa AF: 0.854 Hom.: 198746

Bravo AF: 0.887

TwinsUK AF: 0.838 AC: 3109

ALSPAC AF: 0.841 AC: 3240

ESP6500AA AF: 0.963 AC: 4245

ESP6500EA AF: 0.842 AC: 7240

ExAC AF: 0.869 AC: 105469

Asia WGS AF: 0.869 AC: 3022 AN: 3478

EpiCase AF: 0.835

EpiControl AF: 0.833

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.65	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	1.3
DANN	Benign	0.41
DEOGEN2	Benign	0.010	T
Eigen	Benign	-2.0
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.024	N
LIST_S2	Benign	0.14	T
MetaRNN	Benign	0.0000010	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-1.1	N
PhyloP100		-0.037
PrimateAI	Benign	0.35	T
PROVEAN	Benign	1.6	N
REVEL	Benign	0.17
Sift	Benign	0.74	T
Sift4G	Benign	0.69	T
Polyphen		0.0	B
Vest4		0.030
MPC		0.37
ClinPred		0.00061	T
GERP RS		-0.41
Varity_R		0.026
gMVP		0.35
Mutation Taster		=98/2	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7792760; hg19: chr7-45004063; COSMIC: COSV107260449; COSMIC: COSV107260449;