chr20-13279896-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_080826.2(ISM1):c.641A>C(p.Tyr214Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080826.2 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISM1 | NM_080826.2 | c.641A>C | p.Tyr214Ser | missense_variant, splice_region_variant | 3/6 | ENST00000262487.5 | |
ISM1 | XM_017027680.2 | c.641A>C | p.Tyr214Ser | missense_variant, splice_region_variant | 3/7 | ||
TASP1 | XR_001754319.3 | n.1369+36074T>G | intron_variant, non_coding_transcript_variant | ||||
TASP1 | XR_007067463.1 | n.1370-13714T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISM1 | ENST00000262487.5 | c.641A>C | p.Tyr214Ser | missense_variant, splice_region_variant | 3/6 | 5 | NM_080826.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.641A>C (p.Y214S) alteration is located in exon 3 (coding exon 3) of the ISM1 gene. This alteration results from a A to C substitution at nucleotide position 641, causing the tyrosine (Y) at amino acid position 214 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.