9-131128416-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005085.4(NUP214):c.326C>T(p.Ala109Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,613,618 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005085.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00754 AC: 1147AN: 152106Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00217 AC: 546AN: 251270Hom.: 10 AF XY: 0.00182 AC XY: 247AN XY: 135806
GnomAD4 exome AF: 0.000801 AC: 1170AN: 1461394Hom.: 16 Cov.: 31 AF XY: 0.000669 AC XY: 486AN XY: 726972
GnomAD4 genome AF: 0.00752 AC: 1145AN: 152224Hom.: 13 Cov.: 32 AF XY: 0.00705 AC XY: 525AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at