chr7-44969726-G-A

Variant names:

• chr7-44969726-G-A
• rs3735484
• NM_033054.3:c.1482C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_033054.3(MYO1G):​c.1482C>T​(p.His494His) 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
• Publications: 13 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 -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1G	NM_033054.3	MANE Select	c.1482C>T	p.His494His	synonymous	Exon 11 of 22	NP_149043.2	B0I1T2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1G	ENST00000258787.12	TSL:1 MANE Select	c.1482C>T	p.His494His	synonymous	Exon 11 of 22	ENSP00000258787.7	B0I1T2-1
	MYO1G	ENST00000495831.5	TSL:1	n.*1144C>T		non_coding_transcript_exon	Exon 10 of 21	ENSP00000417650.1	F8WAS7
	MYO1G	ENST00000495831.5	TSL:1	n.*1144C>T		3_prime_UTR	Exon 10 of 21	ENSP00000417650.1	F8WAS7

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

GnomAD2 exomes AF: 0.407 AC: 101626 AN: 249390 AF XY: 0.410

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 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

African (AFR) AF: 0.306 AC: 10237 AN: 33410

American (AMR) AF: 0.367 AC: 16387 AN: 44686

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 12239 AN: 26078

East Asian (EAS) AF: 0.652 AC: 25848 AN: 39652

South Asian (SAS) AF: 0.413 AC: 35540 AN: 86076

European-Finnish (FIN) AF: 0.364 AC: 19096 AN: 52400

Middle Eastern (MID) AF: 0.463 AC: 2100 AN: 4540

European-Non Finnish (NFE) AF: 0.403 AC: 447727 AN: 1111336

Other (OTH) AF: 0.419 AC: 25217 AN: 60198

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

African (AFR) AF: 0.313 AC: 12945 AN: 41412

American (AMR) AF: 0.378 AC: 5761 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1591 AN: 3462

East Asian (EAS) AF: 0.617 AC: 3156 AN: 5118

South Asian (SAS) AF: 0.408 AC: 1964 AN: 4818

European-Finnish (FIN) AF: 0.354 AC: 3743 AN: 10584

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.402 AC: 27240 AN: 67750

Other (OTH) AF: 0.417 AC: 876 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.5
DANN	Benign	0.32
PhyloP100		0.32
Mutation Taster		=74/26	polymorphism

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

Other links and lift over

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