1-25815762-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020451.3(SELENON):c.*44G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,603,776 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_020451.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00256 AC: 389AN: 152194Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00265 AC: 649AN: 245064Hom.: 5 AF XY: 0.00276 AC XY: 368AN XY: 133376
GnomAD4 exome AF: 0.00112 AC: 1630AN: 1451464Hom.: 12 Cov.: 28 AF XY: 0.00121 AC XY: 878AN XY: 722694
GnomAD4 genome AF: 0.00257 AC: 392AN: 152312Hom.: 2 Cov.: 33 AF XY: 0.00252 AC XY: 188AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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SEPN1-related disorder Benign:1
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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at