9-100292669-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014425.5(INVS):c.2412T>G(p.Ser804=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,778 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. S804S) has been classified as 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.2412T>G | p.Ser804= | synonymous_variant | 14/17 | ENST00000262457.7 | |
INVS | NM_001318381.2 | c.2124T>G | p.Ser708= | synonymous_variant | 15/18 | ||
INVS | NM_001318382.2 | c.1434T>G | p.Ser478= | synonymous_variant | 14/17 | ||
INVS | NR_134606.2 | n.2561T>G | non_coding_transcript_exon_variant | 14/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INVS | ENST00000262457.7 | c.2412T>G | p.Ser804= | synonymous_variant | 14/17 | 1 | NM_014425.5 | A2 | |
INVS | ENST00000262456.6 | c.2179+233T>G | intron_variant | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151900Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248964Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134790
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461878Hom.: 0 Cov.: 60 AF XY: 0.0000151 AC XY: 11AN XY: 727242
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151900Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74162
ClinVar
Submissions by phenotype
Nephronophthisis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at