rs7928656
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_023930.4(KCTD14):c.*356T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 276,114 control chromosomes in the GnomAD database, including 6,498 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.23 ( 4486 hom., cov: 32)
Exomes 𝑓: 0.16 ( 2012 hom. )
Consequence
KCTD14
NM_023930.4 3_prime_UTR
NM_023930.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.54
Genes affected
KCTD14 (HGNC:23295): (potassium channel tetramerization domain containing 14) Predicted to be involved in protein homooligomerization. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD14 | NM_023930.4 | c.*356T>C | 3_prime_UTR_variant | 2/2 | ENST00000353172.6 | ||
NDUFC2-KCTD14 | NM_001203262.2 | c.*1034T>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD14 | ENST00000353172.6 | c.*356T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_023930.4 | P1 | ||
ENST00000533697.1 | n.428A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.227 AC: 34462AN: 152026Hom.: 4481 Cov.: 32
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GnomAD4 exome AF: 0.164 AC: 20335AN: 123970Hom.: 2012 Cov.: 0 AF XY: 0.164 AC XY: 10630AN XY: 64956
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GnomAD4 genome ? AF: 0.227 AC: 34511AN: 152144Hom.: 4486 Cov.: 32 AF XY: 0.231 AC XY: 17217AN XY: 74384
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at