NM_024704.5:c.1979G>T

Variant names:

• chr20-16380023-C-A
• rs138901840
• NM_024704.5:c.1979G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024704.5(KIF16B):​c.1979G>T​(p.Arg660Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R660H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KIF16B NM_024704.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.82
• 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.1979G>T	p.Arg660Leu	missense	Exon 19 of 26	NP_078980.3
	KIF16B	NM_001410853.1		c.2012G>T	p.Arg671Leu	missense	Exon 20 of 23	NP_001397782.1
	KIF16B	NM_001199866.2		c.1979G>T	p.Arg660Leu	missense	Exon 19 of 23	NP_001186795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	ENST00000354981.7	TSL:1 MANE Select	c.1979G>T	p.Arg660Leu	missense	Exon 19 of 26	ENSP00000347076.2
	KIF16B	ENST00000408042.5	TSL:1	c.1979G>T	p.Arg660Leu	missense	Exon 19 of 23	ENSP00000384164.1
	KIF16B	ENST00000636835.1	TSL:1	c.1979G>T	p.Arg660Leu	missense	Exon 19 of 25	ENSP00000489838.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00 AC: 0 AN: 235562 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Uncertain	0.031	T
BayesDel_noAF	Benign	-0.19
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.39	T
Eigen	Pathogenic	0.74
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.95	D
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.42	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.5	M
PhyloP100		4.8
PrimateAI	Uncertain	0.60	T
PROVEAN	Uncertain	-3.4	D
REVEL	Benign	0.13
Sift	Benign	0.032	D
Sift4G	Benign	0.31	T
Polyphen		1.0	D
Vest4		0.71
MutPred		0.35		Gain of ubiquitination at K659 (P = 0.0231)
MVP		0.56
MPC		0.58
ClinPred		0.98	D
GERP RS		5.3
Varity_R		0.48
gMVP		0.46
Mutation Taster		=233/67	polymorphism

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: rs138901840; hg19: chr20-16360668;