rs56212569
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024312.5(GNPTAB):c.2611G>A(p.Gly871Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00204 in 1,613,954 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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. G871G) has been classified as Likely benign.
Frequency
Consequence
NM_024312.5 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 |
---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.2611G>A | p.Gly871Ser | missense_variant | 13/21 | ENST00000299314.12 | |
GNPTAB | XM_011538731.3 | c.2530G>A | p.Gly844Ser | missense_variant | 13/21 | ||
GNPTAB | XM_006719593.4 | c.2611G>A | p.Gly871Ser | missense_variant | 13/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.2611G>A | p.Gly871Ser | missense_variant | 13/21 | 1 | NM_024312.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0112 AC: 1698AN: 152170Hom.: 40 Cov.: 33
GnomAD3 exomes AF: 0.00310 AC: 778AN: 251246Hom.: 14 AF XY: 0.00233 AC XY: 316AN XY: 135802
GnomAD4 exome AF: 0.00108 AC: 1585AN: 1461666Hom.: 31 Cov.: 33 AF XY: 0.000909 AC XY: 661AN XY: 727160
GnomAD4 genome AF: 0.0112 AC: 1711AN: 152288Hom.: 41 Cov.: 33 AF XY: 0.0109 AC XY: 815AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 26, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 01, 2020 | - - |
Mucolipidosis type II Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 04, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Pseudo-Hurler polydystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 24, 2014 | - - |
Pseudo-Hurler polydystrophy;C2673377:Mucolipidosis type II Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at