7-129389056-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015328.4(AHCYL2):c.476C>T(p.Ala159Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,600,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015328.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AHCYL2 | NM_015328.4 | c.476C>T | p.Ala159Val | missense_variant, splice_region_variant | 3/17 | ENST00000325006.8 | NP_056143.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AHCYL2 | ENST00000325006.8 | c.476C>T | p.Ala159Val | missense_variant, splice_region_variant | 3/17 | 1 | NM_015328.4 | ENSP00000315931.3 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151702Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000838 AC: 2AN: 238662Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 129068
GnomAD4 exome AF: 0.00000966 AC: 14AN: 1449010Hom.: 0 Cov.: 36 AF XY: 0.0000125 AC XY: 9AN XY: 720636
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151702Hom.: 0 Cov.: 31 AF XY: 0.0000540 AC XY: 4AN XY: 74050
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.476C>T (p.A159V) alteration is located in exon 3 (coding exon 3) of the AHCYL2 gene. This alteration results from a C to T substitution at nucleotide position 476, causing the alanine (A) at amino acid position 159 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