Variant rs73237446 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_138444.4(KCTD12):c.261C>T(p.Phe87=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00856 in 1,597,208 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0063 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0088 ( 82 hom. )

Consequence

KCTD12
NM_138444.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.32

Variant links:

Genes affected

KCTD12 (HGNC:14678): (potassium channel tetramerization domain containing 12) Enables identical protein binding activity. Predicted to be involved in protein homooligomerization. Predicted to act upstream of or within regulation of G protein-coupled receptor signaling pathway. Predicted to be located in cell projection. Predicted to be part of receptor complex. Predicted to be active in postsynaptic membrane and presynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]

KCTD12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 13-76885888-G-A is Benign according to our data. Variant chr13-76885888-G-A is described in ClinVar as [Benign]. Clinvar id is 789220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.32 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD12	NM_138444.4 linkuse as main transcript	c.261C>T	p.Phe87=	synonymous_variant	1/1	ENST00000377474.4	NP_612453.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD12	ENST00000377474.4 linkuse as main transcript	c.261C>T	p.Phe87=	synonymous_variant	1/1		NM_138444.4	ENSP00000366694	P1

Frequencies

GnomAD3 genomes

AF:

0.00631

AC:

960

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00142

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.00621

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00188

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00966

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.00632

AC:

1427

AN:

225942

Hom.:

AF XY:

0.00626

AC XY:

784

AN XY:

125142

show subpopulations

Gnomad AFR exome

AF:

0.00153

Gnomad AMR exome

AF:

0.00519

Gnomad ASJ exome

AF:

0.0167

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00116

Gnomad FIN exome

AF:

0.00220

Gnomad NFE exome

AF:

0.00940

Gnomad OTH exome

AF:

0.00716

GnomAD4 exome

AF:

0.00880

AC:

12719

AN:

1444846

Hom.:

Cov.:

AF XY:

0.00852

AC XY:

6124

AN XY:

719160

show subpopulations

Gnomad4 AFR exome

AF:

0.00231

Gnomad4 AMR exome

AF:

0.00542

Gnomad4 ASJ exome

AF:

0.0155

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.000930

Gnomad4 FIN exome

AF:

0.00251

Gnomad4 NFE exome

AF:

0.0100

Gnomad4 OTH exome

AF:

0.00955

GnomAD4 genome

AF:

0.00628

AC:

957

AN:

152362

Hom.:

Cov.:

AF XY:

0.00552

AC XY:

411

AN XY:

74512

show subpopulations

Gnomad4 AFR

AF:

0.00142

Gnomad4 AMR

AF:

0.00620

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00103

Gnomad4 FIN

AF:

0.00188

Gnomad4 NFE

AF:

0.00964

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00581

Hom.:

Bravo

AF:

0.00641

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0112

EpiControl

AF:

0.0115

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 03, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.97

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