rs780406236
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014425.5(INVS):c.1131G>A(p.Leu377Leu) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Consequence
INVS
NM_014425.5 synonymous
NM_014425.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.96
Genes affected
INVS (HGNC:17870): (inversin) This gene encodes a protein containing multiple ankyrin domains and two IQ calmodulin-binding domains. The encoded protein may function in renal tubular development and function, and in left-right axis determination. This protein interacts with nephrocystin and infers a connection between primary cilia function and left-right axis determination. A similar protein in mice interacts with calmodulin. Mutations in this gene have been associated with nephronophthisis type 2. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 9-100252335-G-A is Benign according to our data. Variant chr9-100252335-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 260405.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INVS | NM_014425.5 | c.1131G>A | p.Leu377Leu | synonymous_variant | Exon 9 of 17 | ENST00000262457.7 | NP_055240.2 | |
INVS | NM_001318381.2 | c.843G>A | p.Leu281Leu | synonymous_variant | Exon 10 of 18 | NP_001305310.1 | ||
INVS | NM_001318382.2 | c.153G>A | p.Leu51Leu | synonymous_variant | Exon 9 of 17 | NP_001305311.1 | ||
INVS | NR_134606.2 | n.1329G>A | non_coding_transcript_exon_variant | Exon 9 of 17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INVS | ENST00000262457.7 | c.1131G>A | p.Leu377Leu | synonymous_variant | Exon 9 of 17 | 1 | NM_014425.5 | ENSP00000262457.2 | ||
INVS | ENST00000262456.6 | c.1131G>A | p.Leu377Leu | synonymous_variant | Exon 9 of 18 | 5 | ENSP00000262456.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at