22-42554962-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014509.5(SERHL2):c.47C>T(p.Ala16Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000674 in 148,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014509.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERHL2 | NM_014509.5 | c.47C>T | p.Ala16Val | missense_variant | Exon 2 of 12 | ENST00000327678.10 | NP_055324.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000674 AC: 1AN: 148358Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000151 AC: 2AN: 132712Hom.: 0 AF XY: 0.0000285 AC XY: 2AN XY: 70162
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000274 AC: 3AN: 1095934Hom.: 0 Cov.: 16 AF XY: 0.00000363 AC XY: 2AN XY: 550348
GnomAD4 genome AF: 0.00000674 AC: 1AN: 148358Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 72254
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.47C>T (p.A16V) alteration is located in exon 2 (coding exon 2) of the SERHL2 gene. This alteration results from a C to T substitution at nucleotide position 47, causing the alanine (A) at amino acid position 16 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