chr3-130703748-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014602.3(PIK3R4):c.3073A>T(p.Met1025Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000306 in 1,613,402 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014602.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3R4 | NM_014602.3 | c.3073A>T | p.Met1025Leu | missense_variant | 13/20 | ENST00000356763.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3R4 | ENST00000356763.8 | c.3073A>T | p.Met1025Leu | missense_variant | 13/20 | 1 | NM_014602.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00160 AC: 244AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000418 AC: 105AN: 251092Hom.: 0 AF XY: 0.000309 AC XY: 42AN XY: 135732
GnomAD4 exome AF: 0.000170 AC: 248AN: 1461090Hom.: 1 Cov.: 29 AF XY: 0.000142 AC XY: 103AN XY: 726912
GnomAD4 genome ? AF: 0.00161 AC: 245AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.00166 AC XY: 124AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at