rs3735484

Positions:

• chr7-44969726-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_033054.3(MYO1G):​c.1482C>T​(p.His494=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,610,064 control chromosomes in the GnomAD database, including 133,975 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 0.38 (11211 hom., cov: 32)
  • Exomes 𝑓: 0.41 (122764 hom.)
• Consequence: MYO1G NM_033054.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP7: Synonymous conserved (PhyloP=0.316 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1G	NM_033054.3	c.1482C>T	p.His494=	synonymous_variant	11/22	ENST00000258787.12
MYO1G	XR_007060129.1	n.1536C>T		non_coding_transcript_exon_variant	11/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1G	ENST00000258787.12	c.1482C>T	p.His494=	synonymous_variant	11/22	1	NM_033054.3	P1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57701 AN: 151568 Hom.: 11202 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.413

GnomAD3 exomes AF: 0.407 AC: 101626 AN: 249390 Hom.: 21325 AF XY: 0.410 AC XY: 55364 AN XY: 135072

Gnomad AFR exome AF: 0.315

Gnomad AMR exome AF: 0.362

Gnomad ASJ exome AF: 0.471

Gnomad EAS exome AF: 0.610

Gnomad SAS exome AF: 0.410

Gnomad FIN exome AF: 0.357

Gnomad NFE exome AF: 0.405

Gnomad OTH exome AF: 0.403

GnomAD4 exome AF: 0.408 AC: 594391 AN: 1458376 Hom.: 122764 Cov.: 52 AF XY: 0.409 AC XY: 296762 AN XY: 725488

Gnomad4 AFR exome AF: 0.306

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.469

Gnomad4 EAS exome AF: 0.652

Gnomad4 SAS exome AF: 0.413

Gnomad4 FIN exome AF: 0.364

Gnomad4 NFE exome AF: 0.403

Gnomad4 OTH exome AF: 0.419

GnomAD4 genome AF: 0.381 AC: 57749 AN: 151688 Hom.: 11211 Cov.: 32 AF XY: 0.380 AC XY: 28197 AN XY: 74162

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.417

Alfa AF: 0.387 Hom.: 4736

Bravo AF: 0.383

Asia WGS AF: 0.487 AC: 1693 AN: 3478

EpiCase AF: 0.406

EpiControl AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.5
DANN	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs3735484; hg19: chr7-45009325; COSMIC: COSV51853455;