rs1859137

chr16-2700454-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018992.4(KCTD5):c.549+538A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,084 control chromosomes in the GnomAD database, including 16,284 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 0.45 (16284 hom., cov: 33)
• Consequence: KCTD5 NM_018992.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

Genes affected

KCTD5 (HGNC:21423): (potassium channel tetramerization domain containing 5) Enables identical protein binding activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCTD5	NM_018992.4	c.549+538A>G		intron_variant		ENST00000301738.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCTD5	ENST00000301738.9	c.549+538A>G		intron_variant		1	NM_018992.4	P1
KCTD5	ENST00000564195.1	c.457+538A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68929 AN: 151966 Hom.: 16265 Cov.: 33

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.454 AC: 68982 AN: 152084 Hom.: 16284 Cov.: 33 AF XY: 0.449 AC XY: 33397 AN XY: 74330

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.0895

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.462

Alfa AF: 0.491 Hom.: 22279

Bravo AF: 0.442

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.8
Dann	Benign	0.54
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

Publications

LitVar

Other links and lift over

dbSNP: rs1859137; hg19: chr16-2750455;