dbSNP rs714948: PVR:c.*834A>C (chr19-44662645-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006505.5(PVR):c.*834A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,318 control chromosomes in the GnomAD database, including 65,482 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 0.93 ( 65427 hom., cov: 31)

Exomes 𝑓: 0.94 ( 55 hom. )

Consequence

PVR
NM_006505.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

29 publications found

Variant links:

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]

PVR links:

CEACAM19 (HGNC:31951): (CEA cell adhesion molecule 19) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CEACAM19 links:

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

CEACAM16-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PVR	NM_006505.5 link	c.*834A>C	3_prime_UTR_variant	Exon 8 of 8	ENST00000425690.8	NP_006496.4	P15151A0A0C4DG49A8K4I1
PVR	NM_001135768.3 link	c.*834A>C	3_prime_UTR_variant	Exon 8 of 8		NP_001129240.1	P15151-2
PVR	NM_001135769.3 link	c.*834A>C	3_prime_UTR_variant	Exon 7 of 7		NP_001129241.1	P15151-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PVR	ENST00000425690.8 link	c.*834A>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_006505.5	ENSP00000402060.2		A0A0C4DG49

Frequencies

GnomAD3 genomes

AF:

0.926

AC:

140828

AN:

152074

Hom.:

65371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.980

Gnomad AMI

AF:

0.862

Gnomad AMR

AF:

0.953

Gnomad ASJ

AF:

0.942

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.978

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.888

Gnomad OTH

AF:

0.933

GnomAD4 exome

AF:

0.937

AC:

118

AN:

126

Hom.:

Cov.:

AF XY:

0.947

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.929

AC:

104

AN:

112

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.581

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.926

AC:

140942

AN:

152192

Hom.:

65427

Cov.:

AF XY:

0.927

AC XY:

68989

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.980

AC:

40705

AN:

41542

American (AMR)

AF:

0.953

AC:

14563

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.942

AC:

3272

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5179

AN:

5180

South Asian (SAS)

AF:

0.977

AC:

4703

AN:

4814

European-Finnish (FIN)

AF:

0.861

AC:

9106

AN:

10582

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.888

AC:

60373

AN:

68010

Other (OTH)

AF:

0.934

AC:

1969

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

527

1055

1582

2110

2637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.905

Hom.:

47587

Bravo

AF:

0.936

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.1

(source)

PhyloP100

0.064

PromoterAI

0.0062

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over