19-44657628-T-G

Variant names:

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

Variant summary

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

The NM_006505.5(PVR):​c.843-134T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: 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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PVR	NM_006505.5	c.843-134T>G		intron_variant	Intron 4 of 7	ENST00000425690.8	NP_006496.4
PVR	NM_001135770.4	c.843-134T>G		intron_variant	Intron 4 of 5		NP_001129242.2
PVR	NM_001135768.3	c.843-134T>G		intron_variant	Intron 4 of 7		NP_001129240.1
PVR	NM_001135769.3	c.843-134T>G		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>G		intron_variant	Intron 4 of 7	1	NM_006505.5	ENSP00000402060.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 637812 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 328280

African (AFR) AF: 0.00 AC: 0 AN: 15126

American (AMR) AF: 0.00 AC: 0 AN: 20838

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14990

East Asian (EAS) AF: 0.00 AC: 0 AN: 30488

South Asian (SAS) AF: 0.00 AC: 0 AN: 51824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34234

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2410

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 435856

Other (OTH) AF: 0.00 AC: 0 AN: 32046

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.40
PhyloP100		-3.3

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;