20-16388359-A-T

Variant names:

• chr20-16388359-A-T
• rs2208056
• NM_024704.5:c.1785-6612T>A

Variant summary

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

The NM_024704.5(KIF16B):​c.1785-6612T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,128 control chromosomes in the GnomAD database, including 38,221 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 0.70 (38221 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF16B	NM_024704.5	c.1785-6612T>A		intron_variant	Intron 17 of 25	ENST00000354981.7	NP_078980.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF16B	ENST00000354981.7	c.1785-6612T>A		intron_variant	Intron 17 of 25	1	NM_024704.5	ENSP00000347076.2

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106095 AN: 152010 Hom.: 38153 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.698 AC: 106230 AN: 152128 Hom.: 38221 Cov.: 32 AF XY: 0.697 AC XY: 51854 AN XY: 74350

African (AFR) AF: 0.840 AC: 34888 AN: 41518

American (AMR) AF: 0.701 AC: 10719 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2198 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5142 AN: 5174

South Asian (SAS) AF: 0.794 AC: 3832 AN: 4826

European-Finnish (FIN) AF: 0.545 AC: 5753 AN: 10556

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.611 AC: 41525 AN: 67978

Other (OTH) AF: 0.681 AC: 1437 AN: 2110

Alfa AF: 0.671 Hom.: 4289

Bravo AF: 0.716

Asia WGS AF: 0.879 AC: 3041 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.48
DANN	Benign	0.58
PhyloP100		-1.6
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: rs2208056; hg19: chr20-16369004;