NM_000030.3:c.26C>A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_000030.3(AGXT):c.26C>A(p.Thr9Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00888 in 1,611,766 control chromosomes in the GnomAD database, including 80 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 (★★).
Frequency
Consequence
NM_000030.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00711 AC: 1080AN: 151974Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00919 AC: 2204AN: 239930Hom.: 18 AF XY: 0.00945 AC XY: 1233AN XY: 130504
GnomAD4 exome AF: 0.00906 AC: 13227AN: 1459678Hom.: 74 Cov.: 31 AF XY: 0.00908 AC XY: 6596AN XY: 726058
GnomAD4 genome AF: 0.00709 AC: 1079AN: 152088Hom.: 6 Cov.: 33 AF XY: 0.00678 AC XY: 504AN XY: 74354
ClinVar
Submissions by phenotype
Primary hyperoxaluria, type I Uncertain:1Benign:3
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Benign:4
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This variant is associated with the following publications: (PMID: 28969594, 27884173, 15849466, 21228398, 20981092, 17495019) -
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AGXT: BP4, BS2 -
not specified Benign:3
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at