7-100342684-C-T

Variant names:

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

Variant summary

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

The ENST00000473757.5(STAG3L5P-PVRIG2P-PILRB):​n.346-3181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0791 in 152,208 control chromosomes in the GnomAD database, including 622 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 0.079 (622 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAG3L5P-PVRIG2P-PILRB	NR_036569.1	n.477-3181C>T		intron_variant	Intron 3 of 17
STAG3L5P-PVRIG2P-PILRB	NR_036570.1	n.477-3181C>T		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>T		intron_variant	Intron 3 of 5	1
STAG3L5P-PVRIG2P-PILRB	ENST00000310771.8	n.428-3181C>T		intron_variant	Intron 3 of 17	2
STAG3L5P-PVRIG2P-PILRB	ENST00000444874.5	n.299-3181C>T		intron_variant	Intron 3 of 16	2

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12045 AN: 152090 Hom.: 623 Cov.: 31

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0791 AC: 12039 AN: 152208 Hom.: 622 Cov.: 31 AF XY: 0.0782 AC XY: 5820 AN XY: 74418

African (AFR) AF: 0.0200 AC: 832 AN: 41544

American (AMR) AF: 0.0754 AC: 1154 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1343 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7936 AN: 67986

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0918 Hom.: 605

Bravo AF: 0.0728

Asia WGS AF: 0.0220 AC: 76 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism (auto)

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;