12-54497899-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005337.5(NCKAP1L):c.102+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000647 in 1,391,484 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_005337.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCKAP1L | ENST00000293373.11 | c.102+8T>C | splice_region_variant, intron_variant | 1 | NM_005337.5 | ENSP00000293373.6 | ||||
NCKAP1L | ENST00000547500.1 | n.126+8T>C | splice_region_variant, intron_variant | 2 | ||||||
NCKAP1L | ENST00000548221.5 | n.102+8T>C | splice_region_variant, intron_variant | 2 | ENSP00000447246.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251224Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135794
GnomAD4 exome AF: 0.00000647 AC: 9AN: 1391484Hom.: 0 Cov.: 23 AF XY: 0.00000574 AC XY: 4AN XY: 696558
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 09, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at