1-20708615-C-G

Variant names:

• chr1-20708615-C-G
• rs6426644
• NM_001122819.3:c.670+1024G>C

Variant summary

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

The NM_001122819.3(KIF17):​c.670+1024G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,048 control chromosomes in the GnomAD database, including 28,512 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 0.61 (28512 hom., cov: 32)
• Consequence: KIF17 NM_001122819.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF17	NM_001122819.3	c.670+1024G>C		intron_variant	Intron 4 of 14	ENST00000400463.8	NP_001116291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF17	ENST00000400463.8	c.670+1024G>C		intron_variant	Intron 4 of 14	1	NM_001122819.3	ENSP00000383311.3
KIF17	ENST00000247986.2	c.670+1024G>C		intron_variant	Intron 4 of 14	1		ENSP00000247986.2
KIF17	ENST00000375044.5	c.370+1024G>C		intron_variant	Intron 4 of 14	1		ENSP00000364184.1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92865 AN: 151930 Hom.: 28503 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.611 AC: 92922 AN: 152048 Hom.: 28512 Cov.: 32 AF XY: 0.608 AC XY: 45213 AN XY: 74320

African (AFR) AF: 0.582 AC: 24112 AN: 41456

American (AMR) AF: 0.577 AC: 8807 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1920 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2752 AN: 5158

South Asian (SAS) AF: 0.489 AC: 2362 AN: 4826

European-Finnish (FIN) AF: 0.694 AC: 7338 AN: 10572

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43764 AN: 67980

Other (OTH) AF: 0.582 AC: 1230 AN: 2114

Alfa AF: 0.553 Hom.: 1702

Bravo AF: 0.601

Asia WGS AF: 0.532 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.75
DANN	Benign	0.63
PhyloP100		-0.37
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: rs6426644; hg19: chr1-21035108;