22-19180775-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007098.4(CLTCL1):c.4859G>A(p.Arg1620His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00929 in 1,613,786 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_007098.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00725 AC: 1103AN: 152198Hom.: 17 Cov.: 34
GnomAD3 exomes AF: 0.0119 AC: 2961AN: 249178Hom.: 59 AF XY: 0.0140 AC XY: 1893AN XY: 135204
GnomAD4 exome AF: 0.00950 AC: 13886AN: 1461470Hom.: 175 Cov.: 31 AF XY: 0.0107 AC XY: 7747AN XY: 727030
GnomAD4 genome AF: 0.00722 AC: 1099AN: 152316Hom.: 17 Cov.: 34 AF XY: 0.00769 AC XY: 573AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
CLTCL1: BP4, BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at