Genetic Variant KCTD20:c.*2532T>C (chr6-36489707-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_173562.5(KCTD20):c.*2532T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,016 control chromosomes in the GnomAD database, including 6,373 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 0.27 ( 6372 hom., cov: 32)

Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

KCTD20
NM_173562.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.953

Publications

19 publications found

Variant links:

Genes affected

KCTD20 (HGNC:21052): (potassium channel tetramerization domain containing 20) Predicted to enable identical protein binding activity. Predicted to be involved in positive regulation of phosphorylation. Predicted to be integral component of membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

KCTD20 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173562.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KCTD20	NM_173562.5	MANE Select	c.*2532T>C	3_prime_UTR	Exon 8 of 8	NP_775833.2
KCTD20	NM_001286580.2		c.*2532T>C	3_prime_UTR	Exon 7 of 7	NP_001273509.1	Q7Z5Y7-3
KCTD20	NM_001286579.2		c.*2532T>C	3_prime_UTR	Exon 5 of 5	NP_001273508.1	Q7Z5Y7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KCTD20	ENST00000373731.7	TSL:1 MANE Select	c.*2532T>C	3_prime_UTR	Exon 8 of 8	ENSP00000362836.2	Q7Z5Y7-1
KCTD20	ENST00000449081.6	TSL:1	c.*2532T>C	3_prime_UTR	Exon 5 of 5	ENSP00000412205.2	Q7Z5Y7-2
KCTD20	ENST00000901245.1		c.*2532T>C	3_prime_UTR	Exon 10 of 10	ENSP00000571304.1

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41149

AN:

151896

Hom.:

6356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.242

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.264

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Age Distribution

Exome Hom

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:

0.271

AC:

41214

AN:

152014

Hom.:

6372

Cov.:

AF XY:

0.271

AC XY:

20152

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.419

AC:

17347

AN:

41428

American (AMR)

AF:

0.247

AC:

3768

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

764

AN:

3470

East Asian (EAS)

AF:

0.389

AC:

2013

AN:

5176

South Asian (SAS)

AF:

0.210

AC:

1011

AN:

4820

European-Finnish (FIN)

AF:

0.242

AC:

2555

AN:

10564

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12978

AN:

67968

Other (OTH)

AF:

0.265

AC:

560

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1471

2942

4414

5885

7356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.192

Hom.:

14204

Bravo

AF:

0.282

Asia WGS

AF:

0.279

AC:

970

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.76

(source)

DANN

Benign

0.60

PhyloP100

-0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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