12-109471709-G-C

Position:

• chr12-109471709-G-C

Variant summary

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

The NM_031954.5(KCTD10):​c.4-1981C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,078 control chromosomes in the GnomAD database, including 2,990 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 0.19 (2990 hom., cov: 32)
• Consequence: KCTD10 NM_031954.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

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]

KCTD10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD10	NM_031954.5	c.4-1981C>G		intron_variant		ENST00000228495.11	NP_114160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD10	ENST00000228495.11	c.4-1981C>G		intron_variant		1	NM_031954.5	ENSP00000228495.6

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29001 AN: 151960 Hom.: 2984 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.191 AC: 29030 AN: 152078 Hom.: 2990 Cov.: 32 AF XY: 0.189 AC XY: 14054 AN XY: 74348

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.219

Alfa AF: 0.117 Hom.: 243

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.19

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: rs10850219; hg19: chr12-109909514; COSMIC: COSV57327314; COSMIC: COSV57327314;