6-36489707-T-A

Variant names:

• chr6-36489707-T-A
• rs1061632
• NM_173562.5:c.*2532T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_173562.5(KCTD20):​c.*2532T>A variant causes a 3 prime UTR 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 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 19 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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.*2532T>A		3_prime_UTR	Exon 8 of 8	NP_775833.2
	KCTD20	NM_001286580.2		c.*2532T>A		3_prime_UTR	Exon 7 of 7	NP_001273509.1	Q7Z5Y7-3
	KCTD20	NM_001286579.2		c.*2532T>A		3_prime_UTR	Exon 5 of 5	NP_001273508.1	Q7Z5Y7-2

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 14204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.50
DANN	Benign	0.62
PhyloP100		-0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1061632; hg19: chr6-36457484;