chr2-54255794-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001003937.3(TSPYL6):c.358A>G(p.Thr120Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 1,613,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001003937.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPYL6 | NM_001003937.3 | c.358A>G | p.Thr120Ala | missense_variant | 1/1 | ENST00000317802.9 | |
ACYP2 | NM_001320586.2 | c.405-48894T>C | intron_variant | ENST00000607452.6 | |||
LOC105374610 | XR_007086321.1 | n.1296-16510A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPYL6 | ENST00000317802.9 | c.358A>G | p.Thr120Ala | missense_variant | 1/1 | NM_001003937.3 | P1 | ||
ACYP2 | ENST00000607452.6 | c.405-48894T>C | intron_variant | 2 | NM_001320586.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249352Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135302
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461626Hom.: 0 Cov.: 33 AF XY: 0.000125 AC XY: 91AN XY: 727122
GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.358A>G (p.T120A) alteration is located in exon 1 (coding exon 1) of the TSPYL6 gene. This alteration results from a A to G substitution at nucleotide position 358, causing the threonine (T) at amino acid position 120 to be replaced by an alanine (A). 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