rs4814475

Positions:

• chr20-16344624-G-A
• chr20-16344624-G-T

Variant summary

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

The NM_024704.5(KIF16B):​c.3622-8609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,108 control chromosomes in the GnomAD database, including 3,821 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 (3821 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

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 = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF16B	NM_024704.5	c.3622-8609C>T		intron_variant		ENST00000354981.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF16B	ENST00000354981.7	c.3622-8609C>T		intron_variant		1	NM_024704.5	P1
KIF16B	ENST00000636835.1	c.3469-8609C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31480 AN: 151990 Hom.: 3808 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.207 AC: 31511 AN: 152108 Hom.: 3821 Cov.: 32 AF XY: 0.213 AC XY: 15834 AN XY: 74366

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.223

Alfa AF: 0.210 Hom.: 1855

Bravo AF: 0.206

Asia WGS AF: 0.456 AC: 1585 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.51

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: rs4814475; hg19: chr20-16325269;