rs34565987
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP3BP4BP6_Very_StrongBS2
The NM_024642.5(GALNT12):c.1301C>T(p.Pro434Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,614,128 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P434T) has been classified as Uncertain significance.
Frequency
Consequence
NM_024642.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT12 | NM_024642.5 | c.1301C>T | p.Pro434Leu | missense_variant | 7/10 | ENST00000375011.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT12 | ENST00000375011.4 | c.1301C>T | p.Pro434Leu | missense_variant | 7/10 | 1 | NM_024642.5 | P1 | |
GALNT12 | ENST00000615204.1 | n.163C>T | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00104 AC: 158AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000258 AC: 65AN: 251480Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135916
GnomAD4 exome AF: 0.0000971 AC: 142AN: 1461812Hom.: 2 Cov.: 32 AF XY: 0.0000811 AC XY: 59AN XY: 727214
GnomAD4 genome ? AF: 0.00104 AC: 158AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.00103 AC XY: 77AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Nov 28, 2022 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | 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