chr4-39407446-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_175737.4(KLB):c.497T>C(p.Val166Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000605 in 1,614,212 control chromosomes in the GnomAD database, including 5 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 Likely benign (★★).
Frequency
Consequence
NM_175737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLB | NM_175737.4 | c.497T>C | p.Val166Ala | missense_variant | 1/5 | ENST00000257408.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLB | ENST00000257408.5 | c.497T>C | p.Val166Ala | missense_variant | 1/5 | 1 | NM_175737.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00321 AC: 488AN: 152234Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000746 AC: 187AN: 250622Hom.: 0 AF XY: 0.000552 AC XY: 75AN XY: 135770
GnomAD4 exome AF: 0.000335 AC: 489AN: 1461860Hom.: 1 Cov.: 32 AF XY: 0.000309 AC XY: 225AN XY: 727226
GnomAD4 genome ? AF: 0.00320 AC: 488AN: 152352Hom.: 4 Cov.: 32 AF XY: 0.00318 AC XY: 237AN XY: 74492
ClinVar
Submissions by phenotype
KLB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at