20-16555769-C-T

Position:

• chr20-16555769-C-T

Variant summary

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

The NM_024704.5(KIF16B):​c.47+17460G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,076 control chromosomes in the GnomAD database, including 3,161 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 0.20 (3161 hom., cov: 33)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

Genes affected

KIF16B (HGNC:15869): (kinesin family member 16B) The protein encoded by this gene is a kinesin-like protein that may be involved in intracellular trafficking. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF16B	NM_024704.5	c.47+17460G>A		intron_variant		ENST00000354981.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF16B	ENST00000354981.7	c.47+17460G>A		intron_variant		1	NM_024704.5	P1
KIF16B	ENST00000408042.5	c.47+17460G>A		intron_variant		1
KIF16B	ENST00000636835.1	c.47+17460G>A		intron_variant		1
KIF16B	ENST00000635823.2	c.47+17460G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30219 AN: 151958 Hom.: 3152 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.199 AC: 30261 AN: 152076 Hom.: 3161 Cov.: 33 AF XY: 0.197 AC XY: 14614 AN XY: 74356

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0646

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.179

Alfa AF: 0.170 Hom.: 2218

Bravo AF: 0.208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.18

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: rs6044112; hg19: chr20-16536414;