NM_001397246.1:c.*53C>G

Variant names:

• chr7-100221304-C-G
• rs705867
• NM_001397246.1:c.*53C>G

Variant summary

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

The NM_001397246.1(PVRIG):​c.*53C>G variant causes a 3 prime UTR 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PVRIG NM_001397246.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 20 publications found

Genes affected

PVRIG (HGNC:32190): (PVR related immunoglobulin domain containing) Enables phosphatase binding activity and signaling receptor activity. Involved in negative regulation of T cell receptor signaling pathway. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000292277 (HGNC:):

CASTOR3P (HGNC:29954): (CASTOR family member 3, pseudogene) Predicted to be involved in cellular response to L-arginine and negative regulation of TORC1 signaling. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001397246.1. 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
	PVRIG	NM_001397246.1	MANE Select	c.*53C>G		3_prime_UTR	Exon 5 of 5	NP_001384175.1	A0A8V8TN58
	PVRIG	NM_024070.3		c.*53C>G		3_prime_UTR	Exon 6 of 6	NP_076975.2	Q6DKI7
	PVRIG	NM_001387134.1		c.*53C>G		3_prime_UTR	Exon 5 of 5	NP_001374063.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVRIG	ENST00000699088.1	MANE Select	c.*53C>G		3_prime_UTR	Exon 5 of 5	ENSP00000514123.1	A0A8V8TN58
	PVRIG	ENST00000317271.3	TSL:1	c.*53C>G		3_prime_UTR	Exon 7 of 7	ENSP00000316675.2	Q6DKI7
	ENSG00000292277	ENST00000710637.1		n.*2353C>G		non_coding_transcript_exon	Exon 9 of 9	ENSP00000518392.1	A0AA34QVW2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1231528 Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0 AN XY: 602432

African (AFR) AF: 0.00 AC: 0 AN: 28008

American (AMR) AF: 0.00 AC: 0 AN: 22164

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18756

East Asian (EAS) AF: 0.00 AC: 0 AN: 36586

South Asian (SAS) AF: 0.00 AC: 0 AN: 64042

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32394

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5134

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 972482

Other (OTH) AF: 0.00 AC: 0 AN: 51962

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 28777

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.53
PhyloP100		-0.054
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs705867; hg19: chr7-99818927;