rs773546298
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The ENST00000375011.4(GALNT12):āc.679C>Gā(p.Leu227Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000919 in 1,588,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L227Q) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000375011.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT12 | NM_024642.5 | c.679C>G | p.Leu227Val | missense_variant | 3/10 | ENST00000375011.4 | NP_078918.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT12 | ENST00000375011.4 | c.679C>G | p.Leu227Val | missense_variant | 3/10 | 1 | NM_024642.5 | ENSP00000364150 | P1 | |
GALNT12 | ENST00000610463.1 | c.*110C>G | 3_prime_UTR_variant, NMD_transcript_variant | 2/4 | 4 | ENSP00000477657 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000425 AC: 86AN: 202154Hom.: 0 AF XY: 0.000276 AC XY: 30AN XY: 108656
GnomAD4 exome AF: 0.0000822 AC: 118AN: 1435986Hom.: 0 Cov.: 32 AF XY: 0.0000632 AC XY: 45AN XY: 711912
GnomAD4 genome AF: 0.000184 AC: 28AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74364
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | May 25, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at