17-11379432-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.818C>T(p.Ala273Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000721 in 1,387,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.818C>T | p.Ala273Val | missense_variant | 3/6 | ENST00000441885.8 | |
SHISA6 | NM_001173462.2 | c.818C>T | p.Ala273Val | missense_variant | 3/5 | ||
SHISA6 | NM_001173461.2 | c.799+115906C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA6 | ENST00000441885.8 | c.818C>T | p.Ala273Val | missense_variant | 3/6 | 5 | NM_207386.4 | ||
SHISA6 | ENST00000432116.7 | c.818C>T | p.Ala273Val | missense_variant | 3/5 | 1 | |||
SHISA6 | ENST00000409168.7 | c.799+115906C>T | intron_variant | 1 | P1 | ||||
SHISA6 | ENST00000343478.7 | c.302C>T | p.Ala101Val | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.21e-7 AC: 1AN: 1387416Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 684164
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.818C>T (p.A273V) alteration is located in exon 3 (coding exon 3) of the SHISA6 gene. This alteration results from a C to T substitution at nucleotide position 818, causing the alanine (A) at amino acid position 273 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
Publications
No publications associated with this variant yet.