rs11870474

Variant names:

• chr17-75034715-C-A
• rs11870474
• ENST00000581589.5:c.-384-517C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-75034715-C-A
• chr17-75034715-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000581589.5(KCTD2):​c.-384-517C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0924 in 152,008 control chromosomes in the GnomAD database, including 1,518 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 0.092 (1518 hom., cov: 32)
• Consequence: KCTD2 ENST00000581589.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 5 publications found

Genes affected

KCTD2 (HGNC:21294): (potassium channel tetramerization domain containing 2) Predicted to enable cullin family protein binding activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TRR-CCT2-1 (HGNC:34744):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581589.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD2	NR_110835.2		n.240-517C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD2	ENST00000581589.5	TSL:1	c.-384-517C>A		intron	N/A	ENSP00000464630.1	J3QSC8
	KCTD2	ENST00000584767.5	TSL:1	n.586-517C>A		intron	N/A
	KCTD2	ENST00000579242.5	TSL:4	n.334-517C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14003 AN: 151892 Hom.: 1513 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.00789

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0677

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

GnomAD4 genome AF: 0.0924 AC: 14048 AN: 152008 Hom.: 1518 Cov.: 32 AF XY: 0.0885 AC XY: 6575 AN XY: 74330

African (AFR) AF: 0.267 AC: 11063 AN: 41366

American (AMR) AF: 0.0412 AC: 630 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3470

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5152

South Asian (SAS) AF: 0.00790 AC: 38 AN: 4810

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0280 AC: 1902 AN: 68000

Other (OTH) AF: 0.0680 AC: 143 AN: 2104

Alfa AF: 0.0380 Hom.: 579

Bravo AF: 0.102

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11870474;

hg19: chr17-73030810;