chr12-109959933-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_057169.5(GIT2):āc.1013A>Gā(p.Asn338Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00061 in 1,613,430 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_057169.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIT2 | NM_057169.5 | c.1013A>G | p.Asn338Ser | missense_variant | 12/20 | ENST00000355312.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIT2 | ENST00000355312.8 | c.1013A>G | p.Asn338Ser | missense_variant | 12/20 | 1 | NM_057169.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00143 AC: 218AN: 152060Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000685 AC: 172AN: 251266Hom.: 0 AF XY: 0.000619 AC XY: 84AN XY: 135810
GnomAD4 exome AF: 0.000524 AC: 766AN: 1461252Hom.: 0 Cov.: 29 AF XY: 0.000534 AC XY: 388AN XY: 726992
GnomAD4 genome AF: 0.00143 AC: 218AN: 152178Hom.: 1 Cov.: 32 AF XY: 0.00133 AC XY: 99AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at