rs3762053

Variant names:

• chr8-94490326-T-G
• rs3762053
• NM_015496.5:c.5141-244A>C

Variant summary

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

The NM_015496.5(VIRMA):​c.5141-244A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,086 control chromosomes in the GnomAD database, including 2,070 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 0.15 (2070 hom., cov: 32)
• Consequence: VIRMA NM_015496.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 4 publications found

Genes affected

VIRMA (HGNC:24500): (vir like m6A methyltransferase associated) Enables RNA binding activity. Involved in mRNA alternative polyadenylation and mRNA methylation. Located in cytosol and nuclear speck. Colocalizes with RNA N6-methyladenosine methyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015496.5. 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
	VIRMA	NM_015496.5	MANE Select	c.5141-244A>C		intron	N/A	NP_056311.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIRMA	ENST00000297591.10	TSL:1 MANE Select	c.5141-244A>C		intron	N/A	ENSP00000297591.5	Q69YN4-1
	VIRMA	ENST00000521080.5	TSL:1	n.5988-244A>C		intron	N/A
	VIRMA	ENST00000522263.5	TSL:1	n.*542-244A>C		intron	N/A	ENSP00000429909.1	H0YBN5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22388 AN: 151968 Hom.: 2067 Cov.: 32

Gnomad AFR AF: 0.0501

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.175

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22396 AN: 152086 Hom.: 2070 Cov.: 32 AF XY: 0.152 AC XY: 11261 AN XY: 74326

African (AFR) AF: 0.0502 AC: 2086 AN: 41520

American (AMR) AF: 0.195 AC: 2981 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3470

East Asian (EAS) AF: 0.0644 AC: 333 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4812

European-Finnish (FIN) AF: 0.164 AC: 1733 AN: 10546

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12494 AN: 67980

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.173 Hom.: 6510

Bravo AF: 0.142

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.34
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3762053; hg19: chr8-95502554;