NM_024704.5:c.47+17460G>A

Variant names:

• chr20-16555769-C-T
• rs6044112
• NM_024704.5:c.47+17460G>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.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
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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.47+17460G>A		intron	N/A	NP_078980.3
	KIF16B	NM_001410853.1		c.47+17460G>A		intron	N/A	NP_001397782.1	A0A1B0GVS8
	KIF16B	NM_001199866.2		c.47+17460G>A		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.47+17460G>A		intron	N/A	ENSP00000347076.2	Q96L93-1
	KIF16B	ENST00000408042.5	TSL:1	c.47+17460G>A		intron	N/A	ENSP00000384164.1	Q96L93-2
	KIF16B	ENST00000636835.1	TSL:1	c.47+17460G>A		intron	N/A	ENSP00000489838.1	A0A1B0GTU3

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

African (AFR) AF: 0.266 AC: 11043 AN: 41446

American (AMR) AF: 0.206 AC: 3150 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3468

East Asian (EAS) AF: 0.0646 AC: 335 AN: 5186

South Asian (SAS) AF: 0.186 AC: 900 AN: 4826

European-Finnish (FIN) AF: 0.124 AC: 1315 AN: 10586

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12381 AN: 67964

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.185 Hom.: 3827

Bravo AF: 0.208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.18
PhyloP100		-0.89
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: rs6044112; hg19: chr20-16536414;