chr20-16383948-C-T

Variant names:

• chr20-16383948-C-T
• rs6034465
• NM_024704.5:c.1785-2201G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024704.5(KIF16B):​c.1785-2201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,060 control chromosomes in the GnomAD database, including 3,846 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 0.21 (3846 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF16B	NM_024704.5	c.1785-2201G>A		intron_variant	Intron 17 of 25	ENST00000354981.7	NP_078980.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF16B	ENST00000354981.7	c.1785-2201G>A		intron_variant	Intron 17 of 25	1	NM_024704.5	ENSP00000347076.2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31803 AN: 151942 Hom.: 3834 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.210 AC: 31857 AN: 152060 Hom.: 3846 Cov.: 32 AF XY: 0.213 AC XY: 15799 AN XY: 74330

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.231

Alfa AF: 0.173 Hom.: 1550

Bravo AF: 0.215

Asia WGS AF: 0.451 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.071
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs6034465; hg19: chr20-16364593;