1-112619070-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017744.5(ST7L):c.44C>T(p.Ala15Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000213 in 1,613,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017744.5 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 |
---|---|---|---|---|---|---|---|
ST7L | NM_017744.5 | c.44C>T | p.Ala15Val | missense_variant | 1/15 | ENST00000358039.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7L | ENST00000358039.9 | c.44C>T | p.Ala15Val | missense_variant | 1/15 | 1 | NM_017744.5 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000158 AC: 39AN: 247050Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134568
GnomAD4 exome AF: 0.000197 AC: 288AN: 1461340Hom.: 0 Cov.: 31 AF XY: 0.000182 AC XY: 132AN XY: 726970
GnomAD4 genome AF: 0.000361 AC: 55AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.44C>T (p.A15V) alteration is located in exon 1 (coding exon 1) of the ST7L gene. This alteration results from a C to T substitution at nucleotide position 44, causing the alanine (A) at amino acid position 15 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