rs10410651

Variant names:

• chr19-44657628-T-C
• rs10410651
• NM_006505.5:c.843-134T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-44657628-T-C
• chr19-44657628-T-G

Variant summary

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

The NM_006505.5(PVR):​c.843-134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 788,402 control chromosomes in the GnomAD database, including 46,789 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 0.40 (15247 hom., cov: 32)
  • Exomes 𝑓: 0.30 (31542 hom.)
• Consequence: PVR NM_006505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33
• Publications: 9 publications found

Genes affected

PVR (HGNC:9705): (PVR cell adhesion molecule) The protein encoded by this gene is a transmembrane glycoprotein belonging to the immunoglobulin superfamily. The external domain mediates cell attachment to the extracellular matrix molecule vitronectin, while its intracellular domain interacts with the dynein light chain Tctex-1/DYNLT1. The gene is specific to the primate lineage, and serves as a cellular receptor for poliovirus in the first step of poliovirus replication. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PVR	NM_006505.5	c.843-134T>C		intron_variant	Intron 4 of 7	ENST00000425690.8	NP_006496.4
PVR	NM_001135770.4	c.843-134T>C		intron_variant	Intron 4 of 5		NP_001129242.2
PVR	NM_001135768.3	c.843-134T>C		intron_variant	Intron 4 of 7		NP_001129240.1
PVR	NM_001135769.3	c.843-134T>C		intron_variant	Intron 4 of 6		NP_001129241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PVR	ENST00000425690.8	c.843-134T>C		intron_variant	Intron 4 of 7	1	NM_006505.5	ENSP00000402060.2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61026 AN: 151776 Hom.: 15216 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.299 AC: 190539 AN: 636506 Hom.: 31542 AF XY: 0.303 AC XY: 99220 AN XY: 327610

African (AFR) AF: 0.713 AC: 10757 AN: 15096

American (AMR) AF: 0.260 AC: 5408 AN: 20786

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 4604 AN: 14966

East Asian (EAS) AF: 0.481 AC: 14647 AN: 30422

South Asian (SAS) AF: 0.409 AC: 21161 AN: 51750

European-Finnish (FIN) AF: 0.235 AC: 8037 AN: 34186

Middle Eastern (MID) AF: 0.289 AC: 694 AN: 2404

European-Non Finnish (NFE) AF: 0.265 AC: 115217 AN: 434906

Other (OTH) AF: 0.313 AC: 10014 AN: 31990

GnomAD4 genome AF: 0.402 AC: 61102 AN: 151896 Hom.: 15247 Cov.: 32 AF XY: 0.399 AC XY: 29624 AN XY: 74240

African (AFR) AF: 0.713 AC: 29552 AN: 41426

American (AMR) AF: 0.301 AC: 4593 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2370 AN: 5140

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4814

European-Finnish (FIN) AF: 0.232 AC: 2451 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18074 AN: 67910

Other (OTH) AF: 0.363 AC: 765 AN: 2110

Alfa AF: 0.256 Hom.: 1186

Bravo AF: 0.418

Asia WGS AF: 0.449 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.30
PhyloP100		-3.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs10410651; hg19: chr19-45160896; COSMIC: COSV51824041; COSMIC: COSV51824041;