20-16471944-G-C

Variant names:

• chr20-16471944-G-C
• rs6043984
• NM_024704.5:c.1302+22347C>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+22347C>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 152,122 control chromosomes in the GnomAD database, including 3,806 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 (3806 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 0 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 (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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	NM_024704.5	MANE Select	c.1302+22347C>G		intron	N/A	NP_078980.3
	KIF16B	NM_001410853.1		c.1302+22347C>G		intron	N/A	NP_001397782.1
	KIF16B	NM_001199866.2		c.1302+22347C>G		intron	N/A	NP_001186795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	ENST00000354981.7	TSL:1 MANE Select	c.1302+22347C>G		intron	N/A	ENSP00000347076.2
	KIF16B	ENST00000408042.5	TSL:1	c.1302+22347C>G		intron	N/A	ENSP00000384164.1
	KIF16B	ENST00000636835.1	TSL:1	c.1302+22347C>G		intron	N/A	ENSP00000489838.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33585 AN: 152004 Hom.: 3798 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.252

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: 33618 AN: 152122 Hom.: 3806 Cov.: 32 AF XY: 0.219 AC XY: 16321 AN XY: 74360

African (AFR) AF: 0.209 AC: 8665 AN: 41500

American (AMR) AF: 0.258 AC: 3946 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5174

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1934 AN: 10562

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15370 AN: 67992

Other (OTH) AF: 0.214 AC: 453 AN: 2112

Alfa AF: 0.222 Hom.: 469

Bravo AF: 0.224

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		0.046
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6043984; hg19: chr20-16452589;