rs203709

Positions:

• chr19-44658298-T-A
• chr19-44658298-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006505.5(PVR):​c.991+388T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,182 control chromosomes in the GnomAD database, including 17,785 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 0.42 (17785 hom., cov: 33)
• Consequence: PVR NM_006505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVR	NM_006505.5	c.991+388T>A		intron_variant		ENST00000425690.8	NP_006496.4
PVR	NM_001135768.3	c.991+388T>A		intron_variant			NP_001129240.1
PVR	NM_001135769.3	c.991+388T>A		intron_variant			NP_001129241.1
PVR	NM_001135770.4	c.991+388T>A		intron_variant			NP_001129242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVR	ENST00000425690.8	c.991+388T>A		intron_variant		1	NM_006505.5	ENSP00000402060	P2
CEACAM16-AS1	ENST00000662585.1	n.476-25679A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64543 AN: 152064 Hom.: 17739 Cov.: 33

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.425 AC: 64636 AN: 152182 Hom.: 17785 Cov.: 33 AF XY: 0.420 AC XY: 31267 AN XY: 74400

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.379

Alfa AF: 0.367 Hom.: 1629

Bravo AF: 0.443

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.74

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: rs203709; hg19: chr19-45161566;