1-6593537-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014851.4(KLHL21):c.1622G>T(p.Ser541Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014851.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL21 | ENST00000377658.8 | c.1622G>T | p.Ser541Ile | missense_variant | Exon 4 of 4 | 1 | NM_014851.4 | ENSP00000366886.4 | ||
KLHL21 | ENST00000496707.5 | c.521G>T | p.Ser174Ile | missense_variant | Exon 4 of 4 | 1 | ENSP00000468710.1 | |||
KLHL21 | ENST00000377663 | c.*1828G>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000366891.3 | ||||
KLHL21 | ENST00000467612.5 | c.521G>T | p.Ser174Ile | missense_variant | Exon 4 of 4 | 3 | ENSP00000466089.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250964Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135782
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461610Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727124
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1622G>T (p.S541I) alteration is located in exon 4 (coding exon 4) of the KLHL21 gene. This alteration results from a G to T substitution at nucleotide position 1622, causing the serine (S) at amino acid position 541 to be replaced by an isoleucine (I). 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