chr3-129137145-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000273541.12(ISY1):c.470C>T(p.Ala157Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000501 in 327,294 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000273541.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISY1 | NM_020701.4 | c.419-2191C>T | intron_variant | ENST00000393295.8 | |||
ISY1-RAB43 | NM_001204890.2 | c.419-2191C>T | intron_variant | ||||
ISY1 | NM_001199469.2 | c.470C>T | p.Ala157Val | missense_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISY1 | ENST00000393295.8 | c.419-2191C>T | intron_variant | 1 | NM_020701.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000231 AC: 35AN: 151814Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 1AN: 6238Hom.: 0 AF XY: 0.000327 AC XY: 1AN XY: 3054
GnomAD4 exome AF: 0.000736 AC: 129AN: 175362Hom.: 0 Cov.: 4 AF XY: 0.000681 AC XY: 57AN XY: 83694
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 151932Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2022 | The c.470C>T (p.A157V) alteration is located in exon 8 (coding exon 8) of the ISY1 gene. This alteration results from a C to T substitution at nucleotide position 470, causing the alanine (A) at amino acid position 157 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at