rs539606269
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_002499.4(NEO1):c.725-6T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,574,664 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002499.4 splice_region, 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: 0.000197 AC: 30AN: 152066Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000573 AC: 123AN: 214716Hom.: 3 AF XY: 0.000736 AC XY: 86AN XY: 116842
GnomAD4 exome AF: 0.000261 AC: 371AN: 1422480Hom.: 6 Cov.: 31 AF XY: 0.000362 AC XY: 256AN XY: 706854
GnomAD4 genome AF: 0.000197 AC: 30AN: 152184Hom.: 1 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74412
ClinVar
Submissions by phenotype
NEO1-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