chr22-19183443-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007098.4(CLTCL1):c.4774G>A(p.Val1592Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,613,660 control chromosomes in the GnomAD database, including 307 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 same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1592L) has been classified as Benign.
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLTCL1 | NM_007098.4 | c.4774G>A | p.Val1592Met | missense_variant | 30/33 | ENST00000427926.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLTCL1 | ENST00000427926.6 | c.4774G>A | p.Val1592Met | missense_variant | 30/33 | 1 | NM_007098.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00951 AC: 1447AN: 152214Hom.: 34 Cov.: 33
GnomAD3 exomes AF: 0.0169 AC: 4207AN: 248308Hom.: 106 AF XY: 0.0185 AC XY: 2495AN XY: 134828
GnomAD4 exome AF: 0.0114 AC: 16695AN: 1461328Hom.: 273 Cov.: 31 AF XY: 0.0125 AC XY: 9079AN XY: 726936
GnomAD4 genome ? AF: 0.00947 AC: 1442AN: 152332Hom.: 34 Cov.: 33 AF XY: 0.0104 AC XY: 774AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 30448225) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at