chr1-217431329-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018040.5(GPATCH2):āc.1403A>Gā(p.Asn468Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,454,902 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 Uncertain significance (ā ).
Frequency
Consequence
NM_018040.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPATCH2 | NM_018040.5 | c.1403A>G | p.Asn468Ser | missense_variant | 10/10 | ENST00000366935.8 | |
GPATCH2 | XM_011509689.4 | c.1472A>G | p.Asn491Ser | missense_variant | 11/11 | ||
GPATCH2 | XM_011509690.4 | c.1361A>G | p.Asn454Ser | missense_variant | 9/9 | ||
GPATCH2 | XM_017001592.3 | c.1292A>G | p.Asn431Ser | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPATCH2 | ENST00000366935.8 | c.1403A>G | p.Asn468Ser | missense_variant | 10/10 | 2 | NM_018040.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250258Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135364
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454902Hom.: 0 Cov.: 27 AF XY: 0.00000276 AC XY: 2AN XY: 724346
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at