NM_001122819.3:c.1233+1741G>C

Variant names:

• chr1-20696638-C-G
• rs674102
• NM_001122819.3:c.1233+1741G>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.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
• 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=-0.85).
• 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 rank	MANE	Protein	UniProt
KIF17	NM_001122819.3	c.1233+1741G>C		intron_variant	Intron 6 of 14	ENST00000400463.8	NP_001116291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF17	ENST00000400463.8	c.1233+1741G>C		intron_variant	Intron 6 of 14	1	NM_001122819.3	ENSP00000383311.3
KIF17	ENST00000247986.2	c.1233+1741G>C		intron_variant	Intron 6 of 14	1		ENSP00000247986.2
KIF17	ENST00000375044.5	c.933+1741G>C		intron_variant	Intron 6 of 14	1		ENSP00000364184.1
KIF17	ENST00000490034.5	n.61+1741G>C		intron_variant	Intron 1 of 8	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

African (AFR) AF: 0.714 AC: 29496 AN: 41328

American (AMR) AF: 0.475 AC: 7250 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1243 AN: 3466

East Asian (EAS) AF: 0.836 AC: 4266 AN: 5102

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4810

European-Finnish (FIN) AF: 0.492 AC: 5179 AN: 10528

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31156 AN: 67792

Other (OTH) AF: 0.534 AC: 1125 AN: 2108

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
PhyloP100		0.13
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: rs674102; hg19: chr1-21023131;