2-137966915-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006895.3(HNMT):c.137+2287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 151,794 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006895.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00154 AC: 233AN: 151676Hom.: 1 Cov.: 32
GnomAD4 genome AF: 0.00153 AC: 232AN: 151794Hom.: 1 Cov.: 32 AF XY: 0.00163 AC XY: 121AN XY: 74192
ClinVar
Submissions by phenotype
Inherited susceptibility to asthma;C4225220:Intellectual disability, autosomal recessive 51 Uncertain:1
The c.137+2287G>A variant in HNMT has not previously been reported in the literature or public variant repositories (ClinVar and LOVD). The c.137+2287G>A variantis observed in 494 alleles (~0.0015% minor allele frequency with 1 homozygote) in population databases (gnomAD v3.1.2 and TOPMed Freeze 8), with >1% minor allele frequency in two subpopulations. The c.137+2287G>A variant is located in intron 1 of this 5-exon gene, and is moderately predicted to affect mRNA splicing (splice AI=0.57 for acceptor gain, 0.27 for acceptor loss), which might result in exon skipping or full/partial intron retention and lead to loss-of-function via nonsense mediated decay; however, there are no functional studies to support or refute these predictions. Based on available evidence this inherited c.137+2287G>A variant identified in HNMT is classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at