Genetic Variant ENSG00000292277:n.*2353C>G (chr7-100221304-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000710637.1(ENSG00000292277):n.*2353C>G variant causes a non coding transcript exon 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

ENSG00000292277
ENST00000710637.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

20 publications found

Variant links:

Genes affected

ENSG00000292277 (HGNC:):

ENSG00000292277 links:

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]

PVRIG links:

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]

CASTOR3P links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PVRIG	NM_001397246.1 link	c.*53C>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000699088.1	NP_001384175.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ENSG00000292277	ENST00000710637.1 link	n.*2353C>G	non_coding_transcript_exon_variant	Exon 9 of 9		ENSP00000518392.1
PVRIG	ENST00000699088.1 link	c.*53C>G	3_prime_UTR_variant	Exon 5 of 5	NM_001397246.1	ENSP00000514123.1	A0A8V8TN58
ENSG00000292277	ENST00000710637.1 link	n.*2353C>G	3_prime_UTR_variant	Exon 9 of 9		ENSP00000518392.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1231528

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

602432

African (AFR)

AF:

0.00

AC:

AN:

28008

American (AMR)

AF:

0.00

AC:

AN:

22164

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18756

East Asian (EAS)

AF:

0.00

AC:

AN:

36586

South Asian (SAS)

AF:

0.00

AC:

AN:

64042

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32394

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5134

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

972482

Other (OTH)

AF:

0.00

AC:

AN:

51962

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

28777

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over