11-13492477-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000315.4(PTH):c.276G>A(p.Glu92Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00258 in 1,614,114 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000315.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0140 AC: 2128AN: 152158Hom.: 50 Cov.: 32
GnomAD3 exomes AF: 0.00336 AC: 845AN: 251404Hom.: 16 AF XY: 0.00228 AC XY: 310AN XY: 135870
GnomAD4 exome AF: 0.00139 AC: 2039AN: 1461838Hom.: 40 Cov.: 29 AF XY: 0.00125 AC XY: 906AN XY: 727226
GnomAD4 genome AF: 0.0140 AC: 2128AN: 152276Hom.: 50 Cov.: 32 AF XY: 0.0124 AC XY: 922AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:2
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Familial hypoparathyroidism Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at