17-11241631-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207386.4(SHISA6):c.209C>T(p.Ala70Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,346,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A70S) has been classified as Uncertain significance.
Frequency
Consequence
NM_207386.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHISA6 | NM_207386.4 | c.209C>T | p.Ala70Val | missense_variant | 1/6 | ENST00000441885.8 | |
SHISA6 | NM_001173462.2 | c.209C>T | p.Ala70Val | missense_variant | 1/5 | ||
SHISA6 | NM_001173461.2 | c.209C>T | p.Ala70Val | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA6 | ENST00000441885.8 | c.209C>T | p.Ala70Val | missense_variant | 1/6 | 5 | NM_207386.4 | ||
SHISA6 | ENST00000432116.7 | c.209C>T | p.Ala70Val | missense_variant | 1/5 | 1 | |||
SHISA6 | ENST00000409168.7 | c.209C>T | p.Ala70Val | missense_variant | 1/4 | 1 | P1 | ||
ENST00000648331.1 | n.98+334G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000666 AC: 1AN: 150240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 2AN: 12188Hom.: 0 AF XY: 0.000145 AC XY: 1AN XY: 6904
GnomAD4 exome AF: 0.0000259 AC: 31AN: 1195924Hom.: 0 Cov.: 31 AF XY: 0.0000310 AC XY: 18AN XY: 580240
GnomAD4 genome ? AF: 0.00000666 AC: 1AN: 150240Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.209C>T (p.A70V) alteration is located in exon 1 (coding exon 1) of the SHISA6 gene. This alteration results from a C to T substitution at nucleotide position 209, causing the alanine (A) at amino acid position 70 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