20-16473257-T-G

Variant names:

• chr20-16473257-T-G
• rs6043986
• NM_024704.5:c.1302+21034A>C

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+21034A>C 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 152,138 control chromosomes in the GnomAD database, including 3,794 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 (3794 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF16B	NM_024704.5	c.1302+21034A>C		intron_variant	Intron 12 of 25	ENST00000354981.7	NP_078980.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF16B	ENST00000354981.7	c.1302+21034A>C		intron_variant	Intron 12 of 25	1	NM_024704.5	ENSP00000347076.2
KIF16B	ENST00000408042.5	c.1302+21034A>C		intron_variant	Intron 12 of 22	1		ENSP00000384164.1
KIF16B	ENST00000636835.1	c.1302+21034A>C		intron_variant	Intron 12 of 24	1		ENSP00000489838.1
KIF16B	ENST00000635823.2	c.1302+21034A>C		intron_variant	Intron 12 of 22	5		ENSP00000490639.2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33579 AN: 152020 Hom.: 3786 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.221 AC: 33614 AN: 152138 Hom.: 3794 Cov.: 32 AF XY: 0.219 AC XY: 16320 AN XY: 74386

African (AFR) AF: 0.209 AC: 8688 AN: 41512

American (AMR) AF: 0.258 AC: 3940 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5164

South Asian (SAS) AF: 0.220 AC: 1059 AN: 4820

European-Finnish (FIN) AF: 0.185 AC: 1958 AN: 10596

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15317 AN: 67980

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.136 Hom.: 232

Bravo AF: 0.224

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.49
PhyloP100		-0.33
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: rs6043986; hg19: chr20-16453902;