6-36470137-C-A

Variant names:

• chr6-36470137-C-A
• rs534162644
• NM_173562.5:c.40C>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_173562.5(KCTD20):​c.40C>A​(p.Arg14Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: KCTD20 NM_173562.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BP7: Synonymous conserved (PhyloP=0.406 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD20	NM_173562.5	MANE Select	c.40C>A	p.Arg14Arg	synonymous	Exon 2 of 8	NP_775833.2
	KCTD20	NM_001286579.2		c.40C>A	p.Arg14Arg	synonymous	Exon 2 of 5	NP_001273508.1	Q7Z5Y7-2
	KCTD20	NM_001286580.2		c.-122C>A		5_prime_UTR	Exon 2 of 7	NP_001273509.1	Q7Z5Y7-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD20	ENST00000373731.7	TSL:1 MANE Select	c.40C>A	p.Arg14Arg	synonymous	Exon 2 of 8	ENSP00000362836.2	Q7Z5Y7-1
	KCTD20	ENST00000449081.6	TSL:1	c.40C>A	p.Arg14Arg	synonymous	Exon 2 of 5	ENSP00000412205.2	Q7Z5Y7-2
	KCTD20	ENST00000901245.1		c.40C>A	p.Arg14Arg	synonymous	Exon 4 of 10	ENSP00000571304.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251192 AF XY: 0.00000737

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		0.41
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0

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: rs534162644; hg19: chr6-36437914;