20-873061-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_015985.4(ANGPT4):c.1411G>A(p.Asp471Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000235 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015985.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANGPT4 | NM_015985.4 | c.1411G>A | p.Asp471Asn | missense_variant | Exon 9 of 9 | ENST00000381922.5 | NP_057069.1 | |
ANGPT4 | XM_011529239.4 | c.1255G>A | p.Asp419Asn | missense_variant | Exon 8 of 8 | XP_011527541.1 | ||
ANGPT4 | NM_001322809.2 | c.*47G>A | 3_prime_UTR_variant | Exon 8 of 8 | NP_001309738.1 | |||
LOC124904854 | XR_007067485.1 | n.249C>T | non_coding_transcript_exon_variant | Exon 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251308Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135834
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727194
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152274Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at