3-183492223-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_130446.4(KLHL6):c.1570G>T(p.Ala524Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000208 in 1,444,528 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130446.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHL6 | NM_130446.4 | c.1570G>T | p.Ala524Ser | missense_variant | Exon 7 of 7 | ENST00000341319.8 | NP_569713.2 | |
KLHL6 | XM_011513273.4 | c.1189G>T | p.Ala397Ser | missense_variant | Exon 6 of 6 | XP_011511575.1 | ||
KLHL6 | XM_011513274.4 | c.*1984G>T | 3_prime_UTR_variant | Exon 4 of 4 | XP_011511576.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL6 | ENST00000341319.8 | c.1570G>T | p.Ala524Ser | missense_variant | Exon 7 of 7 | 1 | NM_130446.4 | ENSP00000341342.3 | ||
KLHL6 | ENST00000468734.1 | n.1537G>T | non_coding_transcript_exon_variant | Exon 7 of 8 | 1 | ENSP00000433734.1 | ||||
KLHL6 | ENST00000489245.5 | n.2980G>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000426 AC: 1AN: 234904Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127942
GnomAD4 exome AF: 0.00000208 AC: 3AN: 1444528Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 716206
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1570G>T (p.A524S) alteration is located in exon 7 (coding exon 7) of the KLHL6 gene. This alteration results from a G to T substitution at nucleotide position 1570, causing the alanine (A) at amino acid position 524 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at