rs674102

Positions:

• chr1-20696638-C-G
• chr1-20696638-C-T

Variant summary

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

The NM_001122819.3(KIF17):​c.1233+1741G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,610 control chromosomes in the GnomAD database, including 23,904 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 0.55 (23904 hom., cov: 31)
• Consequence: KIF17 NM_001122819.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF17	NM_001122819.3	c.1233+1741G>C		intron_variant		ENST00000400463.8	NP_001116291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF17	ENST00000400463.8	c.1233+1741G>C		intron_variant		1	NM_001122819.3	ENSP00000383311.3
KIF17	ENST00000247986.2	c.1233+1741G>C		intron_variant		1		ENSP00000247986.2
KIF17	ENST00000375044.5	c.933+1741G>C		intron_variant		1		ENSP00000364184.1
KIF17	ENST00000490034.5	n.61+1741G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82919 AN: 151492 Hom.: 23851 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.548 AC: 83031 AN: 151610 Hom.: 23904 Cov.: 31 AF XY: 0.550 AC XY: 40749 AN XY: 74078

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.534

Alfa AF: 0.374 Hom.: 1020

Bravo AF: 0.556

Asia WGS AF: 0.712 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.40

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: rs674102; hg19: chr1-21023131;