2-96344101-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015341.5(NCAPH):c.596-4T>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,609,008 control chromosomes in the GnomAD database, including 11 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 (★).
Frequency
Consequence
NM_015341.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCAPH | NM_015341.5 | c.596-4T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000240423.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAPH | ENST00000240423.9 | c.596-4T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015341.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00148 AC: 225AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00120 AC: 294AN: 245980Hom.: 0 AF XY: 0.00119 AC XY: 158AN XY: 133202
GnomAD4 exome AF: 0.00276 AC: 4021AN: 1456654Hom.: 11 Cov.: 30 AF XY: 0.00269 AC XY: 1949AN XY: 724802
GnomAD4 genome AF: 0.00148 AC: 225AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.00136 AC XY: 101AN XY: 74496
ClinVar
Submissions by phenotype
NCAPH-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 16, 2019 | 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