2-69961291-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_152792.4(ASPRV1):c.146C>T(p.Thr49Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T49A) has been classified as Likely benign.
Frequency
Consequence
NM_152792.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASPRV1 | NM_152792.4 | c.146C>T | p.Thr49Ile | missense_variant | 1/1 | ENST00000320256.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASPRV1 | ENST00000320256.6 | c.146C>T | p.Thr49Ile | missense_variant | 1/1 | NM_152792.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251448Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135892
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727236
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152142Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74324
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at