Genetic Variant NM_001363642.1:c.*709C>A (chr17-7354350-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232

Publications

8 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363642.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD11	NM_001363642.1	MANE Select	c.*709C>A		3_prime_UTR	Exon 1 of 1	NP_001350571.1
	KCTD11	NM_001002914.3		c.*709C>A		3_prime_UTR	Exon 1 of 1	NP_001002914.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KCTD11	ENST00000333751.8	TSL:6 MANE Select	c.*709C>A	3_prime_UTR	Exon 1 of 1	ENSP00000328352.5
KCTD11	ENST00000576980.2	TSL:6	c.*709C>A	3_prime_UTR	Exon 1 of 1	ENSP00000495203.1
ENSG00000263171	ENST00000572417.1	TSL:2	n.275+320G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0945

AC:

14358

AN:

151980

Hom.:

859

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.104

AC XY:

746

AN XY:

7182

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.375

AC:

AN:

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AF:

0.0992

AC:

1460

AN:

14716

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0612

AC:

AN:

196

Other (OTH)

AF:

0.113

AC:

AN:

106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

148

221

295

369

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0946

AC:

14386

AN:

152098

Hom.:

865

Cov.:

AF XY:

0.0951

AC XY:

7070

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.156

AC:

6460

AN:

41462

American (AMR)

AF:

0.0637

AC:

975

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0334

AC:

116

AN:

3468

East Asian (EAS)

AF:

0.164

AC:

849

AN:

5176

South Asian (SAS)

AF:

0.0750

AC:

362

AN:

4828

European-Finnish (FIN)

AF:

0.0992

AC:

1049

AN:

10574

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0640

AC:

4353

AN:

67974

Other (OTH)

AF:

0.0848

AC:

179

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

653

1305

1958

2610

3263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0738

Hom.:

1557

Bravo

AF:

0.0962

Asia WGS

AF:

0.135

AC:

467

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.48

PhyloP100

-0.23

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over