chr2-54255724-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001003937.3(TSPYL6):c.428C>T(p.Ala143Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,882 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.428C>T | p.Ala143Val | missense_variant | 1/1 | ENST00000317802.9 | |
ACYP2 | NM_001320586.2 | c.405-48964G>A | intron_variant | ENST00000607452.6 | |||
LOC105374610 | XR_007086321.1 | n.1296-16440C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPYL6 | ENST00000317802.9 | c.428C>T | p.Ala143Val | missense_variant | 1/1 | NM_001003937.3 | P1 | ||
ACYP2 | ENST00000607452.6 | c.405-48964G>A | intron_variant | 2 | NM_001320586.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249182Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135234
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461666Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727146
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2023 | The c.428C>T (p.A143V) alteration is located in exon 1 (coding exon 1) of the TSPYL6 gene. This alteration results from a C to T substitution at nucleotide position 428, causing the alanine (A) at amino acid position 143 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