Variant chr17-7353006-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001363642.1(KCTD11):c.181G>A(p.Gly61Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0028 in 1,611,554 control chromosomes in the GnomAD database, including 115 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 65 hom., cov: 33)

Exomes 𝑓: 0.0015 ( 50 hom. )

Consequence

KCTD11
NM_001363642.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.81

Variant links:

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]

KCTD11 links:

ENSG00000263171 (HGNC:):

ENSG00000263171 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002516508).

BP6

Variant 17-7353006-G-A is Benign according to our data. Variant chr17-7353006-G-A is described in ClinVar as [Benign]. Clinvar id is 787990.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD11	NM_001363642.1 linkuse as main transcript	c.181G>A	p.Gly61Ser	missense_variant	1/1	ENST00000333751.8	NP_001350571.1
KCTD11	NM_001002914.3 linkuse as main transcript	c.64G>A	p.Gly22Ser	missense_variant	1/1		NP_001002914.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KCTD11	ENST00000333751.8 linkuse as main transcript	c.181G>A	p.Gly61Ser	missense_variant	1/1	6	NM_001363642.1	ENSP00000328352.5	Q693B1-2A0A2U3TZI5
KCTD11	ENST00000576980.2 linkuse as main transcript	c.64G>A	p.Gly22Ser	missense_variant	1/1	6		ENSP00000495203.1	Q693B1-1
ENSG00000263171	ENST00000572417.1 linkuse as main transcript	n.276-174C>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0155

AC:

2362

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0534

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00785

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000118

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.00402

AC:

1004

AN:

249802

Hom.:

AF XY:

0.00287

AC XY:

388

AN XY:

135326

show subpopulations

Gnomad AFR exome

AF:

0.0554

Gnomad AMR exome

AF:

0.00290

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000443

Gnomad OTH exome

AF:

0.00165

GnomAD4 exome

AF:

0.00147

AC:

2142

AN:

1459276

Hom.:

Cov.:

AF XY:

0.00128

AC XY:

927

AN XY:

725452

show subpopulations

Gnomad4 AFR exome

AF:

0.0520

Gnomad4 AMR exome

AF:

0.00323

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000186

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000423

Gnomad4 OTH exome

AF:

0.00309

GnomAD4 genome

AF:

0.0155

AC:

2365

AN:

152278

Hom.:

Cov.:

AF XY:

0.0149

AC XY:

1110

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0533

Gnomad4 AMR

AF:

0.00784

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000118

Gnomad4 OTH

AF:

0.00995

Alfa

AF:

0.00305

Hom.:

Bravo

AF:

0.0179

ESP6500AA

AF:

0.0504

AC:

222

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.00514

AC:

624

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.44

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.24

T;.

Eigen

Benign

-0.21

Eigen_PC

Benign

-0.092

FATHMM_MKL

Uncertain

0.85

LIST_S2

Benign

0.63

T;T

MetaRNN

Benign

0.0025

T;T

MetaSVM

Benign

-0.85

MutationAssessor

Benign

1.9

L;.

PrimateAI

Benign

0.41

REVEL

Benign

0.18

Polyphen

0.11

B;.

MVP

0.76

MPC

0.69

ClinPred

0.0098

GERP RS

3.7

Varity_R

0.19

gMVP

0.82

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over