rs2208059

Variant names:

• chr20-16330665-T-C
• rs2208059
• NM_024704.5:c.3711+5261A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024704.5(KIF16B):​c.3711+5261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,092 control chromosomes in the GnomAD database, including 40,589 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 0.72 (40589 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF16B	NM_024704.5	c.3711+5261A>G		intron_variant	Intron 24 of 25	ENST00000354981.7	NP_078980.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF16B	ENST00000354981.7	c.3711+5261A>G		intron_variant	Intron 24 of 25	1	NM_024704.5	ENSP00000347076.2
KIF16B	ENST00000636835.1	c.3558+5261A>G		intron_variant	Intron 23 of 24	1		ENSP00000489838.1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109944 AN: 151974 Hom.: 40530 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.724 AC: 110066 AN: 152092 Hom.: 40589 Cov.: 32 AF XY: 0.724 AC XY: 53817 AN XY: 74330

African (AFR) AF: 0.840 AC: 34903 AN: 41528

American (AMR) AF: 0.706 AC: 10784 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2283 AN: 3472

East Asian (EAS) AF: 0.965 AC: 4983 AN: 5166

South Asian (SAS) AF: 0.813 AC: 3913 AN: 4812

European-Finnish (FIN) AF: 0.612 AC: 6462 AN: 10564

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44452 AN: 67966

Other (OTH) AF: 0.698 AC: 1472 AN: 2110

Alfa AF: 0.679 Hom.: 151312

Bravo AF: 0.732

Asia WGS AF: 0.875 AC: 3040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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: rs2208059; hg19: chr20-16311310;