rs11790431
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014425.5(INVS):c.2068+31G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,604,612 control chromosomes in the GnomAD database, including 20,449 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.18 ( 3124 hom., cov: 33)
Exomes 𝑓: 0.15 ( 17325 hom. )
Consequence
INVS
NM_014425.5 intron
NM_014425.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.425
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 Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 9-100284634-G-A is Benign according to our data. Variant chr9-100284634-G-A is described in ClinVar as [Benign]. Clinvar id is 260409.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INVS | NM_014425.5 | c.2068+31G>A | intron_variant | ENST00000262457.7 | |||
INVS | NM_001318381.2 | c.1780+31G>A | intron_variant | ||||
INVS | NM_001318382.2 | c.1090+31G>A | intron_variant | ||||
INVS | NR_134606.2 | n.2266+31G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INVS | ENST00000262457.7 | c.2068+31G>A | intron_variant | 1 | NM_014425.5 | A2 | |||
INVS | ENST00000262456.6 | c.2068+31G>A | intron_variant | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.184 AC: 28009AN: 152048Hom.: 3122 Cov.: 33
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GnomAD3 exomes AF: 0.125 AC: 29427AN: 235816Hom.: 2323 AF XY: 0.122 AC XY: 15604AN XY: 128074
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GnomAD4 exome AF: 0.147 AC: 213025AN: 1452446Hom.: 17325 Cov.: 31 AF XY: 0.144 AC XY: 103691AN XY: 722038
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GnomAD4 genome ? AF: 0.184 AC: 28035AN: 152166Hom.: 3124 Cov.: 33 AF XY: 0.179 AC XY: 13306AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at