NM_015001.3:c.-1C>T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_015001.3(SPEN):c.-1C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000279 in 1,453,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_015001.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000172 AC: 26AN: 151408Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000145 AC: 20AN: 137964Hom.: 0 AF XY: 0.000106 AC XY: 8AN XY: 75484
GnomAD4 exome AF: 0.000291 AC: 379AN: 1302190Hom.: 0 Cov.: 30 AF XY: 0.000278 AC XY: 179AN XY: 644640
GnomAD4 genome AF: 0.000172 AC: 26AN: 151408Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 73940
ClinVar
Submissions by phenotype
SPEN-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