chr2-74531539-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013247.5(HTRA2):c.940-58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0169 in 1,612,652 control chromosomes in the GnomAD database, including 2,739 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_013247.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTRA2 | NM_013247.5 | c.940-58G>A | intron_variant | Intron 4 of 7 | ENST00000258080.8 | NP_037379.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 4326AN: 152144Hom.: 397 Cov.: 32
GnomAD3 exomes AF: 0.0507 AC: 12533AN: 247414Hom.: 1434 AF XY: 0.0435 AC XY: 5817AN XY: 133836
GnomAD4 exome AF: 0.0157 AC: 22931AN: 1460390Hom.: 2337 Cov.: 33 AF XY: 0.0151 AC XY: 10937AN XY: 726434
GnomAD4 genome AF: 0.0285 AC: 4341AN: 152262Hom.: 402 Cov.: 32 AF XY: 0.0308 AC XY: 2290AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at