Variant rs1812594 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017634.4(KCTD9):c.1146A>G(p.Leu382Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,579,304 control chromosomes in the GnomAD database, including 33,022 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 0.18 ( 2706 hom., cov: 32)

Exomes 𝑓: 0.20 ( 30316 hom. )

Consequence

KCTD9
NM_017634.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.311

Variant links:

Genes affected

KCTD9 (HGNC:22401): (potassium channel tetramerization domain containing 9) Enables cullin family protein binding activity; identical protein binding activity; and protein self-association. Predicted to be involved in intracellular signal transduction; protein homooligomerization; and protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

KCTD9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=-0.311 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD9	NM_017634.4 linkuse as main transcript	c.1146A>G	p.Leu382Leu	synonymous_variant	12/12	ENST00000221200.9	NP_060104.2	Q7L273

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KCTD9	ENST00000221200.9 linkuse as main transcript	c.1146A>G	p.Leu382Leu	synonymous_variant	12/12	1	NM_017634.4	ENSP00000221200.4	Q7L273
KCTD9	ENST00000710397.1 linkuse as main transcript	c.1266A>G	p.Leu422Leu	synonymous_variant	12/12			ENSP00000518251.1
KCTD9	ENST00000519665.5 linkuse as main transcript	n.*1105A>G		non_coding_transcript_exon_variant	11/11	5		ENSP00000466874.1	K7ENB5
KCTD9	ENST00000519665.5 linkuse as main transcript	n.*1105A>G		3_prime_UTR_variant	11/11	5		ENSP00000466874.1	K7ENB5

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26824

AN:

152080

Hom.:

2701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0864

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.176

GnomAD3 exomes

AF:

0.202

AC:

50621

AN:

250950

Hom.:

5592

AF XY:

0.201

AC XY:

27313

AN XY:

135634

show subpopulations

Gnomad AFR exome

AF:

0.0812

Gnomad AMR exome

AF:

0.200

Gnomad ASJ exome

AF:

0.208

Gnomad EAS exome

AF:

0.279

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.221

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.202

AC:

288228

AN:

1427106

Hom.:

30316

Cov.:

AF XY:

0.201

AC XY:

143117

AN XY:

711828

show subpopulations

Gnomad4 AFR exome

AF:

0.0773

Gnomad4 AMR exome

AF:

0.202

Gnomad4 ASJ exome

AF:

0.206

Gnomad4 EAS exome

AF:

0.211

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.193

GnomAD4 genome

AF:

0.176

AC:

26835

AN:

152198

Hom.:

2706

Cov.:

AF XY:

0.177

AC XY:

13136

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.0863

Gnomad4 AMR

AF:

0.193

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.249

Gnomad4 SAS

AF:

0.134

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.201

Hom.:

1379

Bravo

AF:

0.172

Asia WGS

AF:

0.152

AC:

529

AN:

3478

EpiCase

AF:

0.211

EpiControl

AF:

0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.28

DANN

Benign

0.64

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over