rs3809831

Positions:

• chr17-7354350-C-A
• chr17-7354350-C-T

Variant summary

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

The NM_001363642.1(KCTD11):​c.*709C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 167,144 control chromosomes in the GnomAD database, including 934 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 0.095 (865 hom., cov: 32)
  • Exomes 𝑓: 0.099 (69 hom.)
• Consequence: KCTD11 NM_001363642.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

Genes affected

KCTD11 (HGNC:21302): (potassium channel tetramerization domain containing 11) Enables identical protein binding activity. Predicted to be involved in positive regulation of neuron differentiation. Predicted to act upstream of or within negative regulation of neuroblast proliferation and negative regulation of smoothened signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCTD11	NM_001363642.1	c.*709C>A		3_prime_UTR_variant	1/1	ENST00000333751.8
KCTD11	NM_001002914.3	c.*709C>A		3_prime_UTR_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCTD11	ENST00000333751.8	c.*709C>A		3_prime_UTR_variant	1/1		NM_001363642.1
	ENST00000572417.1	n.275+320G>T		intron_variant, non_coding_transcript_variant		2
KCTD11	ENST00000576980.2	c.*709C>A		3_prime_UTR_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14358 AN: 151980 Hom.: 859 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0828

GnomAD4 exome AF: 0.0989 AC: 1488 AN: 15046 Hom.: 69 Cov.: 0 AF XY: 0.104 AC XY: 746 AN XY: 7182

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.0992

Gnomad4 NFE exome AF: 0.0612

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.0946 AC: 14386 AN: 152098 Hom.: 865 Cov.: 32 AF XY: 0.0951 AC XY: 7070 AN XY: 74364

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0637

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0750

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0848

Alfa AF: 0.0646 Hom.: 467

Bravo AF: 0.0962

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3809831; hg19: chr17-7257669; COSMIC: COSV50136588; COSMIC: COSV50136588;