8-6514712-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001118887.2(ANGPT2):c.994G>A(p.Val332Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,614,072 control chromosomes in the GnomAD database, including 15 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_001118887.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANGPT2 | ENST00000629816.3 | c.994G>A | p.Val332Ile | missense_variant | Exon 6 of 9 | 1 | NM_001118887.2 | ENSP00000486858.2 | ||
MCPH1 | ENST00000344683.10 | c.2214+14783C>T | intron_variant | Intron 12 of 13 | 1 | NM_024596.5 | ENSP00000342924.5 |
Frequencies
GnomAD3 genomes AF: 0.00535 AC: 814AN: 152130Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00139 AC: 350AN: 251462Hom.: 6 AF XY: 0.00100 AC XY: 136AN XY: 135900
GnomAD4 exome AF: 0.000594 AC: 869AN: 1461824Hom.: 10 Cov.: 31 AF XY: 0.000501 AC XY: 364AN XY: 727206
GnomAD4 genome AF: 0.00535 AC: 814AN: 152248Hom.: 5 Cov.: 32 AF XY: 0.00533 AC XY: 397AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at