rs34544607

Variant names:

• chr13-76885615-C-G
• rs34544607
• NM_138444.4:c.534G>C

Your query was ambiguous. Multiple possible variants found:

• chr13-76885615-C-G
• chr13-76885615-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_138444.4(KCTD12):​c.534G>C​(p.Thr178Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0404 in 1,504,778 control chromosomes in the GnomAD database, including 1,442 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 0.039 (130 hom., cov: 32)
  • Exomes 𝑓: 0.041 (1312 hom.)
• Consequence: KCTD12 NM_138444.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0837 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138444.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD12	NM_138444.4	MANE Select	c.534G>C	p.Thr178Thr	synonymous	Exon 1 of 1	NP_612453.1	Q96CX2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD12	ENST00000377474.4	TSL:6 MANE Select	c.534G>C	p.Thr178Thr	synonymous	Exon 1 of 1	ENSP00000366694.2	Q96CX2

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5913 AN: 152126 Hom.: 130 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.0311

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.0425

GnomAD2 exomes AF: 0.0475 AC: 4912 AN: 103406 AF XY: 0.0511

Gnomad AFR exome AF: 0.0578

Gnomad AMR exome AF: 0.0205

Gnomad ASJ exome AF: 0.0886

Gnomad EAS exome AF: 0.000234

Gnomad FIN exome AF: 0.0371

Gnomad NFE exome AF: 0.0443

Gnomad OTH exome AF: 0.0482

GnomAD4 exome AF: 0.0406 AC: 54894 AN: 1352544 Hom.: 1312 Cov.: 31 AF XY: 0.0418 AC XY: 27897 AN XY: 666812

African (AFR) AF: 0.0444 AC: 1290 AN: 29086

American (AMR) AF: 0.0204 AC: 588 AN: 28890

Ashkenazi Jewish (ASJ) AF: 0.0782 AC: 1722 AN: 22010

East Asian (EAS) AF: 0.000114 AC: 4 AN: 35150

South Asian (SAS) AF: 0.0900 AC: 6571 AN: 72988

European-Finnish (FIN) AF: 0.0292 AC: 995 AN: 34106

Middle Eastern (MID) AF: 0.0664 AC: 278 AN: 4188

European-Non Finnish (NFE) AF: 0.0384 AC: 41065 AN: 1069864

Other (OTH) AF: 0.0423 AC: 2381 AN: 56262

GnomAD4 genome AF: 0.0388 AC: 5913 AN: 152234 Hom.: 130 Cov.: 32 AF XY: 0.0393 AC XY: 2925 AN XY: 74420

African (AFR) AF: 0.0423 AC: 1756 AN: 41560

American (AMR) AF: 0.0267 AC: 408 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3472

East Asian (EAS) AF: 0.000583 AC: 3 AN: 5148

South Asian (SAS) AF: 0.0907 AC: 438 AN: 4830

European-Finnish (FIN) AF: 0.0311 AC: 330 AN: 10612

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0370 AC: 2519 AN: 67996

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0419 Hom.: 29

Bravo AF: 0.0378

Asia WGS AF: 0.0370 AC: 127 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34544607; hg19: chr13-77459750;