X-101397714-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001199973.2(RPL36A-HNRNPH2):c.300+2257T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 778,622 control chromosomes in the GnomAD database, including 3 homozygotes. There are 102 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001199973.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00100 AC: 113AN: 112673Hom.: 2 Cov.: 23 AF XY: 0.00164 AC XY: 57AN XY: 34813
GnomAD4 exome AF: 0.000246 AC: 164AN: 665893Hom.: 1 AF XY: 0.000231 AC XY: 45AN XY: 195187
GnomAD4 genome AF: 0.00100 AC: 113AN: 112729Hom.: 2 Cov.: 23 AF XY: 0.00163 AC XY: 57AN XY: 34879
ClinVar
Submissions by phenotype
GLA-related disorder Benign:1
This variant is classified as likely 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