rs28483039

chr19-44645964-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PVR	NM_006505.5	c.80-1259G>A		intron_variant		ENST00000425690.8
PVR	NM_001135768.3	c.80-1259G>A		intron_variant
PVR	NM_001135769.3	c.80-1259G>A		intron_variant
PVR	NM_001135770.4	c.80-1259G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PVR	ENST00000425690.8	c.80-1259G>A		intron_variant		1	NM_006505.5	P2
CEACAM16-AS1	ENST00000662585.1	n.476-13345C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.298

Alfa AF: 0.294 Hom.: 869

Bravo AF: 0.326

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs28483039; hg19: chr19-45149235;