chr12-10379727-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007360.4(KLRK1):āc.214A>Gā(p.Thr72Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 1,610,626 control chromosomes in the GnomAD database, including 520,524 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_007360.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLRK1 | NM_007360.4 | c.214A>G | p.Thr72Ala | missense_variant | 4/8 | ENST00000240618.11 | |
KLRC4-KLRK1 | NM_001199805.1 | c.214A>G | p.Thr72Ala | missense_variant | 9/13 | ||
KLRK1-AS1 | NR_120430.1 | n.393T>C | non_coding_transcript_exon_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLRK1 | ENST00000240618.11 | c.214A>G | p.Thr72Ala | missense_variant | 4/8 | 1 | NM_007360.4 | P1 | |
KLRK1-AS1 | ENST00000500682.1 | n.393T>C | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.747 AC: 113519AN: 151912Hom.: 43277 Cov.: 31
GnomAD3 exomes AF: 0.808 AC: 201579AN: 249454Hom.: 82203 AF XY: 0.812 AC XY: 109435AN XY: 134778
GnomAD4 exome AF: 0.807 AC: 1177745AN: 1458596Hom.: 477226 Cov.: 45 AF XY: 0.810 AC XY: 587957AN XY: 725450
GnomAD4 genome AF: 0.747 AC: 113585AN: 152030Hom.: 43298 Cov.: 31 AF XY: 0.749 AC XY: 55700AN XY: 74324
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at