rs138901840

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-16380023-C-T
• chr20-16380023-C-A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_024704.5(KIF16B):​c.1979G>A​(p.Arg660His) variant causes a missense change. The variant allele was found at a frequency of 0.0000808 in 1,596,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00039 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000048 (0 hom.)
• Consequence: KIF16B NM_024704.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.043049574).

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.1979G>A	p.Arg660His	missense	Exon 19 of 26	NP_078980.3
	KIF16B	NM_001410853.1		c.2012G>A	p.Arg671His	missense	Exon 20 of 23	NP_001397782.1	A0A1B0GVS8
	KIF16B	NM_001199866.2		c.1979G>A	p.Arg660His	missense	Exon 19 of 23	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.1979G>A	p.Arg660His	missense	Exon 19 of 26	ENSP00000347076.2	Q96L93-1
	KIF16B	ENST00000408042.5	TSL:1	c.1979G>A	p.Arg660His	missense	Exon 19 of 23	ENSP00000384164.1	Q96L93-2
	KIF16B	ENST00000636835.1	TSL:1	c.1979G>A	p.Arg660His	missense	Exon 19 of 25	ENSP00000489838.1	A0A1B0GTU3

Frequencies

GnomAD3 genomes AF: 0.000388 AC: 59 AN: 152184 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000140 AC: 33 AN: 235562 AF XY: 0.000134

Gnomad AFR exome AF: 0.00144

Gnomad AMR exome AF: 0.000191

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000921

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000485 AC: 70 AN: 1444110 Hom.: 0 Cov.: 34 AF XY: 0.0000585 AC XY: 42 AN XY: 717362

African (AFR) AF: 0.00122 AC: 39 AN: 32094

American (AMR) AF: 0.000194 AC: 8 AN: 41250

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25202

East Asian (EAS) AF: 0.00 AC: 0 AN: 39584

South Asian (SAS) AF: 0.000145 AC: 12 AN: 82804

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53004

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5652

European-Non Finnish (NFE) AF: 0.00000362 AC: 4 AN: 1105010

Other (OTH) AF: 0.000118 AC: 7 AN: 59510

GnomAD4 genome AF: 0.000387 AC: 59 AN: 152302 Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31 AN XY: 74476

African (AFR) AF: 0.00140 AC: 58 AN: 41564

American (AMR) AF: 0.00 AC: 0 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68038

Other (OTH) AF: 0.00 AC: 0 AN: 2114

Alfa AF: 0.000166 Hom.: 0

Bravo AF: 0.000385

ESP6500AA AF: 0.00159 AC: 7

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000123 AC: 15

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)
-	1	-	Prostate cancer (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.088
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.19
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.16	T
Eigen	Pathogenic	0.75
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.96	D
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.043	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.5	M
PhyloP100		4.8
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-2.3	N
REVEL	Benign	0.13
Sift	Uncertain	0.0030	D
Sift4G	Benign	0.16	T
Polyphen		1.0	D
Vest4		0.63
MVP		0.55
MPC		0.61
ClinPred		0.092	T
GERP RS		5.3
Varity_R		0.32
gMVP		0.27
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; COSMIC: COSV61703348;