4-39407442-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_175737.4(KLB):c.493A>G(p.Thr165Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,614,076 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_175737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLB | NM_175737.4 | c.493A>G | p.Thr165Ala | missense_variant | 1/5 | ENST00000257408.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLB | ENST00000257408.5 | c.493A>G | p.Thr165Ala | missense_variant | 1/5 | 1 | NM_175737.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152220Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000359 AC: 90AN: 250640Hom.: 0 AF XY: 0.000368 AC XY: 50AN XY: 135770
GnomAD4 exome AF: 0.000193 AC: 282AN: 1461856Hom.: 2 Cov.: 32 AF XY: 0.000180 AC XY: 131AN XY: 727226
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152220Hom.: 1 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at