chr5-35012953-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_031900.4(AGXT2):c.1188+1G>A variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,551,610 control chromosomes in the GnomAD database, including 261 homozygotes. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_031900.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1879AN: 152214Hom.: 20 Cov.: 33
GnomAD3 exomes AF: 0.0124 AC: 1933AN: 156400Hom.: 21 AF XY: 0.0123 AC XY: 1015AN XY: 82252
GnomAD4 exome AF: 0.0159 AC: 22251AN: 1399278Hom.: 241 Cov.: 31 AF XY: 0.0157 AC XY: 10862AN XY: 690156
GnomAD4 genome AF: 0.0123 AC: 1875AN: 152332Hom.: 20 Cov.: 33 AF XY: 0.0134 AC XY: 999AN XY: 74488
ClinVar
Submissions by phenotype
not specified Benign:2
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: Frequency in ESP (all): 112/11414=0.98%; Frequency in ESP (EUR): 105/7450=1.4% -
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not provided Benign:2
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AGXT2: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at