rs3099417

Variant names:

• chr8-94541624-C-T
• rs3099417
• NM_015496.5:c.179+2203G>A

Variant summary

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

The NM_015496.5(VIRMA):​c.179+2203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,790 control chromosomes in the GnomAD database, including 1,359 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 0.11 (1359 hom., cov: 31)
• Consequence: VIRMA NM_015496.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIRMA	NM_015496.5	c.179+2203G>A		intron_variant	Intron 2 of 23	ENST00000297591.10	NP_056311.2
VIRMA	NM_183009.3	c.179+2203G>A		intron_variant	Intron 2 of 12		NP_892121.1
VIRMA	XM_047421677.1	c.-827+2203G>A		intron_variant	Intron 3 of 24		XP_047277633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIRMA	ENST00000297591.10	c.179+2203G>A		intron_variant	Intron 2 of 23	1	NM_015496.5	ENSP00000297591.5
VIRMA	ENST00000421249.2	c.179+2203G>A		intron_variant	Intron 2 of 12	1		ENSP00000398390.2
VIRMA	ENST00000519001.1	n.75+2203G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17117 AN: 151674 Hom.: 1359 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.113 AC: 17126 AN: 151790 Hom.: 1359 Cov.: 31 AF XY: 0.112 AC XY: 8294 AN XY: 74180

African (AFR) AF: 0.216 AC: 8930 AN: 41364

American (AMR) AF: 0.0621 AC: 946 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3464

East Asian (EAS) AF: 0.233 AC: 1199 AN: 5142

South Asian (SAS) AF: 0.150 AC: 722 AN: 4810

European-Finnish (FIN) AF: 0.0473 AC: 498 AN: 10532

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4345 AN: 67928

Other (OTH) AF: 0.0924 AC: 195 AN: 2110

Alfa AF: 0.0908 Hom.: 119

Bravo AF: 0.119

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		0.44
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: rs3099417; hg19: chr8-95553852;