chr1-20668459-G-A

Variant names:

• chr1-20668459-G-A
• rs2170336
• NM_001122819.3:c.2790+1962C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001122819.3(KIF17):​c.2790+1962C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,202 control chromosomes in the GnomAD database, including 1,268 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 0.13 (1268 hom., cov: 32)
• Consequence: KIF17 NM_001122819.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 8 publications found

Genes affected

KIF17 (HGNC:19167): (kinesin family member 17) Predicted to enable microtubule binding activity and plus-end-directed microtubule motor activity. Predicted to be involved in anterograde dendritic transport of neurotransmitter receptor complex and cell projection organization. Predicted to act upstream of or within microtubule-based process; protein-containing complex localization; and vesicle-mediated transport. Predicted to be located in microtubule cytoskeleton. Predicted to be part of intraciliary transport particle B and kinesin complex. Predicted to be active in cilium; microtubule cytoskeleton; and neuron projection. [provided by Alliance of Genome Resources, Apr 2022]

KIF17 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF17	NM_001122819.3	c.2790+1962C>T		intron_variant	Intron 13 of 14	ENST00000400463.8	NP_001116291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF17	ENST00000400463.8	c.2790+1962C>T		intron_variant	Intron 13 of 14	1	NM_001122819.3	ENSP00000383311.3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19252 AN: 152084 Hom.: 1263 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.0838

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.127 AC: 19284 AN: 152202 Hom.: 1268 Cov.: 32 AF XY: 0.126 AC XY: 9399 AN XY: 74402

African (AFR) AF: 0.137 AC: 5674 AN: 41508

American (AMR) AF: 0.0901 AC: 1378 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5190

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4828

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10588

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9274 AN: 68006

Other (OTH) AF: 0.121 AC: 255 AN: 2112

Alfa AF: 0.126 Hom.: 2154

Bravo AF: 0.121

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		0.40
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: rs2170336; hg19: chr1-20994952;