5-144393155-C-T

Position:

• chr5-144393155-C-T

Variant summary

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

The NM_020768.4(KCTD16):​c.833-80505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,128 control chromosomes in the GnomAD database, including 52,744 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 0.83 (52744 hom., cov: 31)
• Consequence: KCTD16 NM_020768.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

Genes affected

KCTD16 (HGNC:29244): (potassium channel tetramerization domain containing 16) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD16	NM_020768.4	c.833-80505C>T		intron_variant		ENST00000512467.6	NP_065819.1
KCTD16	NM_001370486.1	c.833-80505C>T		intron_variant			NP_001357415.1
KCTD16	NM_001370487.1	c.833-80505C>T		intron_variant			NP_001357416.1
KCTD16	XM_005268493.3	c.833-80505C>T		intron_variant			XP_005268550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD16	ENST00000512467.6	c.833-80505C>T		intron_variant		1	NM_020768.4	ENSP00000424151.1
KCTD16	ENST00000507359.3	c.833-80505C>T		intron_variant		1		ENSP00000426548.1

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125850 AN: 152010 Hom.: 52691 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.828 AC: 125961 AN: 152128 Hom.: 52744 Cov.: 31 AF XY: 0.830 AC XY: 61719 AN XY: 74376

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.837

Alfa AF: 0.794 Hom.: 8281

Bravo AF: 0.834

Asia WGS AF: 0.833 AC: 2898 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.22

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: rs6580317; hg19: chr5-143772718;