chr10-122462067-T-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_002775.5(HTRA1):āc.415T>Gā(p.Ser139Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000054 in 1,535,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002775.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTRA1 | ENST00000368984.8 | c.415T>G | p.Ser139Ala | missense_variant | Exon 1 of 9 | 1 | NM_002775.5 | ENSP00000357980.3 | ||
HTRA1 | ENST00000648167.1 | c.154+3358T>G | intron_variant | Intron 1 of 8 | ENSP00000498033.1 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000609 AC: 8AN: 131388Hom.: 0 AF XY: 0.0000277 AC XY: 2AN XY: 72118
GnomAD4 exome AF: 0.0000304 AC: 42AN: 1383664Hom.: 0 Cov.: 33 AF XY: 0.0000249 AC XY: 17AN XY: 683052
GnomAD4 genome AF: 0.000269 AC: 41AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 05, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at