4-56809985-C-CT
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001271722.2(SPINK2):c.404dupA(p.Ter135fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,500,592 control chromosomes in the GnomAD database, including 26 homozygotes. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001271722.2 frameshift
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: 0.00667 AC: 1015AN: 152072Hom.: 14 Cov.: 32
GnomAD4 exome AF: 0.000935 AC: 1261AN: 1348402Hom.: 12 Cov.: 30 AF XY: 0.00103 AC XY: 684AN XY: 663834
GnomAD4 genome AF: 0.00666 AC: 1014AN: 152190Hom.: 14 Cov.: 32 AF XY: 0.00643 AC XY: 478AN XY: 74392
ClinVar
Submissions by phenotype
SPINK2-related disorder Benign:1
This variant is classified as 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