chr9-100272966-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014425.5(INVS):c.1674C>A(p.Ala558=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A558A) has been classified as Likely benign.
Frequency
Consequence
NM_014425.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INVS | NM_014425.5 | c.1674C>A | p.Ala558= | synonymous_variant | 12/17 | ENST00000262457.7 | |
INVS | NM_001318381.2 | c.1386C>A | p.Ala462= | synonymous_variant | 13/18 | ||
INVS | NM_001318382.2 | c.696C>A | p.Ala232= | synonymous_variant | 12/17 | ||
INVS | NR_134606.2 | n.1872C>A | non_coding_transcript_exon_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INVS | ENST00000262457.7 | c.1674C>A | p.Ala558= | synonymous_variant | 12/17 | 1 | NM_014425.5 | A2 | |
INVS | ENST00000262456.6 | c.1674C>A | p.Ala558= | synonymous_variant | 12/18 | 5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251472Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135908
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461848Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727234
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74228
ClinVar
Submissions by phenotype
Nephronophthisis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 29, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at