rs13228694

Variant names:

• chr7-100342684-C-G
• rs13228694
• ENST00000473757.5:n.346-3181C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-100342684-C-G
• chr7-100342684-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000473757.5(STAG3L5P-PVRIG2P-PILRB):​n.346-3181C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000592 in 152,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000059 (0 hom., cov: 31)
• Consequence: STAG3L5P-PVRIG2P-PILRB ENST00000473757.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 10 publications found

Genes affected

STAG3L5P-PVRIG2P-PILRB (HGNC:48898): (STAG3L5P-PVRIG2P-PILRB readthrough) This locus represents naturally occurring readthrough transcription among the neighboring LOC101735302 (stromal antigen 3 pseudogene), LOC101752334 (poliovirus receptor related immunoglobulin domain containing pseudogene) and PILRB (paired immunoglobin-like type 2 receptor beta) genes on chromosome 7. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Jun 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAG3L5P-PVRIG2P-PILRB	NR_036569.1	n.477-3181C>G		intron_variant	Intron 3 of 17
STAG3L5P-PVRIG2P-PILRB	NR_036570.1	n.477-3181C>G		intron_variant	Intron 3 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAG3L5P-PVRIG2P-PILRB	ENST00000473757.5	n.346-3181C>G		intron_variant	Intron 3 of 5	1
STAG3L5P-PVRIG2P-PILRB	ENST00000310771.8	n.428-3181C>G		intron_variant	Intron 3 of 17	2
STAG3L5P-PVRIG2P-PILRB	ENST00000444874.5	n.299-3181C>G		intron_variant	Intron 3 of 16	2

Frequencies

GnomAD3 genomes AF: 0.0000592 AC: 9 AN: 152106 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000592 AC: 9 AN: 152106 Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5 AN XY: 74304

African (AFR) AF: 0.0000241 AC: 1 AN: 41424

American (AMR) AF: 0.00 AC: 0 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 68000

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.84
DANN	Benign	0.51
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13228694; hg19: chr7-99940307;