rs2338104

Positions:

• chr12-109457363-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031954.5(KCTD10):​c.527+267G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 341,572 control chromosomes in the GnomAD database, including 52,920 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 0.57 (25961 hom., cov: 33)
  • Exomes 𝑓: 0.52 (26959 hom.)
• Consequence: KCTD10 NM_031954.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

Genes affected

KCTD10 (HGNC:23236): (potassium channel tetramerization domain containing 10) The protein encoded by this gene binds proliferating cell nuclear antigen (PCNA) and may be involved in DNA synthesis and cell proliferation. In addition, the encoded protein may be a tumor suppressor. Several protein-coding and non-protein coding transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD10	NM_031954.5	c.527+267G>C		intron_variant		ENST00000228495.11	NP_114160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD10	ENST00000228495.11	c.527+267G>C		intron_variant		1	NM_031954.5	ENSP00000228495	P1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87038 AN: 151930 Hom.: 25915 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.588

GnomAD4 exome AF: 0.523 AC: 99179 AN: 189524 Hom.: 26959 Cov.: 2 AF XY: 0.521 AC XY: 50813 AN XY: 97504

Gnomad4 AFR exome AF: 0.748

Gnomad4 AMR exome AF: 0.513

Gnomad4 ASJ exome AF: 0.547

Gnomad4 EAS exome AF: 0.324

Gnomad4 SAS exome AF: 0.453

Gnomad4 FIN exome AF: 0.473

Gnomad4 NFE exome AF: 0.547

Gnomad4 OTH exome AF: 0.538

GnomAD4 genome AF: 0.573 AC: 87145 AN: 152048 Hom.: 25961 Cov.: 33 AF XY: 0.564 AC XY: 41917 AN XY: 74360

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.588

Alfa AF: 0.542 Hom.: 12607

Bravo AF: 0.586

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2338104; hg19: chr12-109895168;