rs59362219
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP4_StrongBP6_Very_StrongBS2
The NM_024642.5(GALNT12):c.719C>T(p.Pro240Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,563,076 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P240P) has been classified as Likely benign.
Frequency
Consequence
NM_024642.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT12 | NM_024642.5 | c.719C>T | p.Pro240Leu | missense_variant | 3/10 | ENST00000375011.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT12 | ENST00000375011.4 | c.719C>T | p.Pro240Leu | missense_variant | 3/10 | 1 | NM_024642.5 | P1 | |
GALNT12 | ENST00000610463.1 | c.*150C>T | 3_prime_UTR_variant, NMD_transcript_variant | 2/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152158Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000576 AC: 97AN: 168294Hom.: 1 AF XY: 0.000538 AC XY: 48AN XY: 89156
GnomAD4 exome AF: 0.000192 AC: 271AN: 1410800Hom.: 3 Cov.: 32 AF XY: 0.000171 AC XY: 119AN XY: 697114
GnomAD4 genome ? AF: 0.000302 AC: 46AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 03, 2020 | 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. - |
Breast neoplasm Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ACT Genomics, | Nov 06, 2020 | The allele frequency of this variant c.719C>T (p.Pro240Leu) is 0.0083 in East Asian of gnomAD and 0.011 in East Asian in 1000 Genomes. For the reason, this variant has been classified as Likely Benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2023 | - - |
GALNT12-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at