chr13-45194057-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_198404.3(KCTD4):c.511C>T(p.Arg171Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R171H) has been classified as Uncertain significance.
Frequency
Consequence
NM_198404.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD4 | NM_198404.3 | c.511C>T | p.Arg171Cys | missense_variant | 2/2 | ENST00000379108.2 | |
GTF2F2 | NM_004128.3 | c.305-13367G>A | intron_variant | ENST00000340473.8 | |||
GTF2F2 | XM_011535052.4 | c.382+10579G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD4 | ENST00000379108.2 | c.511C>T | p.Arg171Cys | missense_variant | 2/2 | NM_198404.3 | P1 | ||
GTF2F2 | ENST00000340473.8 | c.305-13367G>A | intron_variant | 1 | NM_004128.3 | P1 | |||
GTF2F2 | ENST00000706694.1 | c.134-13367G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250844Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135546
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 727210
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.511C>T (p.R171C) alteration is located in exon 2 (coding exon 1) of the KCTD4 gene. This alteration results from a C to T substitution at nucleotide position 511, causing the arginine (R) at amino acid position 171 to be replaced by a cysteine (C). 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