9-98831821-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024642.5(GALNT12):c.781G>A(p.Asp261Asn) variant causes a missense change. The variant allele was found at a frequency of 0.012 in 1,614,166 control chromosomes in the GnomAD database, including 164 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. D261H) has been classified as Uncertain significance.
Frequency
Consequence
NM_024642.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT12 | NM_024642.5 | c.781G>A | p.Asp261Asn | missense_variant | 4/10 | ENST00000375011.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT12 | ENST00000375011.4 | c.781G>A | p.Asp261Asn | missense_variant | 4/10 | 1 | NM_024642.5 | P1 | |
GALNT12 | ENST00000610463.1 | c.*212G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0102 AC: 1546AN: 152164Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.0119 AC: 2988AN: 251464Hom.: 22 AF XY: 0.0125 AC XY: 1703AN XY: 135902
GnomAD4 exome AF: 0.0122 AC: 17892AN: 1461884Hom.: 152 Cov.: 32 AF XY: 0.0125 AC XY: 9125AN XY: 727242
GnomAD4 genome AF: 0.0102 AC: 1547AN: 152282Hom.: 12 Cov.: 32 AF XY: 0.0103 AC XY: 769AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 23, 2021 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2016 | This alteration is classified as 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. - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Apr 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at