chr4-39407079-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_175737.4(KLB):c.130C>T(p.Leu44Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,614,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLB | NM_175737.4 | c.130C>T | p.Leu44Phe | missense_variant | 1/5 | ENST00000257408.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLB | ENST00000257408.5 | c.130C>T | p.Leu44Phe | missense_variant | 1/5 | 1 | NM_175737.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000946 AC: 144AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000262 AC: 66AN: 251450Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135898
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461828Hom.: 0 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 727222
GnomAD4 genome ? AF: 0.000945 AC: 144AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00101 AC XY: 75AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at