rs28483039

Variant names:

• chr19-44645964-G-A
• rs28483039
• NM_006505.5:c.80-1259G>A

Variant summary

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

The NM_006505.5(PVR):​c.80-1259G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,826 control chromosomes in the GnomAD database, including 8,525 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 0.32 (8525 hom., cov: 30)
• Consequence: PVR NM_006505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006505.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVR	NM_006505.5	MANE Select	c.80-1259G>A		intron	N/A	NP_006496.4
	PVR	NM_001135770.4		c.80-1259G>A		intron	N/A	NP_001129242.2	A0A0A0MSA9
	PVR	NM_001135768.3		c.80-1259G>A		intron	N/A	NP_001129240.1	P15151-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVR	ENST00000425690.8	TSL:1 MANE Select	c.80-1259G>A		intron	N/A	ENSP00000402060.2	A0A0C4DG49
	PVR	ENST00000406449.8	TSL:1	c.80-1259G>A		intron	N/A	ENSP00000383907.3	A0A0A0MSA9
	PVR	ENST00000971445.1		c.80-1259G>A		intron	N/A	ENSP00000641504.1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48548 AN: 151708 Hom.: 8507 Cov.: 30

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.320 AC: 48607 AN: 151826 Hom.: 8525 Cov.: 30 AF XY: 0.320 AC XY: 23741 AN XY: 74176

African (AFR) AF: 0.474 AC: 19576 AN: 41336

American (AMR) AF: 0.264 AC: 4032 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2384 AN: 5160

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4818

European-Finnish (FIN) AF: 0.217 AC: 2286 AN: 10546

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16673 AN: 67936

Other (OTH) AF: 0.298 AC: 626 AN: 2104

Alfa AF: 0.300 Hom.: 947

Bravo AF: 0.326

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.67
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: rs28483039; hg19: chr19-45149235;