rs3762053

chr8-94490326-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIRMA	NM_015496.5	c.5141-244A>C		intron_variant		ENST00000297591.10
VIRMA	XM_047421677.1	c.4136-244A>C		intron_variant
VIRMA	XM_047421678.1	c.4136-244A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIRMA	ENST00000297591.10	c.5141-244A>C		intron_variant		1	NM_015496.5	P1
VIRMA	ENST00000522263.5	c.*542-244A>C		intron_variant, NMD_transcript_variant		1
VIRMA	ENST00000521080.5	n.5988-244A>C		intron_variant, non_coding_transcript_variant		1
VIRMA	ENST00000517624.1	c.108-244A>C		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0644

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.173

Alfa AF: 0.182 Hom.: 4293

Bravo AF: 0.142

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	13
Dann	Benign	0.34

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

Other links and lift over

dbSNP: rs3762053; hg19: chr8-95502554;