rs6043976

Variant names:

• chr20-16470388-A-C
• rs6043976
• NM_024704.5:c.1302+23903T>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.1302+23903T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,094 control chromosomes in the GnomAD database, including 3,801 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 0.22 (3801 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024704.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	NM_024704.5	MANE Select	c.1302+23903T>G		intron	N/A	NP_078980.3
	KIF16B	NM_001410853.1		c.1302+23903T>G		intron	N/A	NP_001397782.1	A0A1B0GVS8
	KIF16B	NM_001199866.2		c.1302+23903T>G		intron	N/A	NP_001186795.1	Q96L93-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	ENST00000354981.7	TSL:1 MANE Select	c.1302+23903T>G		intron	N/A	ENSP00000347076.2	Q96L93-1
	KIF16B	ENST00000408042.5	TSL:1	c.1302+23903T>G		intron	N/A	ENSP00000384164.1	Q96L93-2
	KIF16B	ENST00000636835.1	TSL:1	c.1302+23903T>G		intron	N/A	ENSP00000489838.1	A0A1B0GTU3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33578 AN: 151978 Hom.: 3793 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.221 AC: 33611 AN: 152094 Hom.: 3801 Cov.: 32 AF XY: 0.219 AC XY: 16314 AN XY: 74346

African (AFR) AF: 0.209 AC: 8655 AN: 41488

American (AMR) AF: 0.258 AC: 3941 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3466

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5168

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1943 AN: 10602

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15368 AN: 67976

Other (OTH) AF: 0.214 AC: 452 AN: 2108

Alfa AF: 0.230 Hom.: 510

Bravo AF: 0.224

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.83
PhyloP100		0.49
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: rs6043976; hg19: chr20-16451033;