chr1-20669007-G-C

Variant names:

• chr1-20669007-G-C
• rs6677104
• NM_001122819.3:c.2790+1414C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001122819.3(KIF17):​c.2790+1414C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 152,146 control chromosomes in the GnomAD database, including 37 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 0.012 (37 hom., cov: 31)
• Consequence: KIF17 NM_001122819.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 1 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=-1.05).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0116 (1767/152146) while in subpopulation AFR AF = 0.0398 (1654/41524). AF 95% confidence interval is 0.0382. There are 37 homozygotes in GnomAd4. There are 819 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 37 Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122819.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF17	NM_001122819.3	MANE Select	c.2790+1414C>G		intron	N/A	NP_001116291.1	Q9P2E2-3
	KIF17	NM_020816.4		c.2793+1414C>G		intron	N/A	NP_065867.2	Q9P2E2-1
	KIF17	NM_001287212.2		c.2493+1414C>G		intron	N/A	NP_001274141.1	A0A0A0MRS8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF17	ENST00000400463.8	TSL:1 MANE Select	c.2790+1414C>G		intron	N/A	ENSP00000383311.3	Q9P2E2-3
	KIF17	ENST00000247986.2	TSL:1	c.2793+1414C>G		intron	N/A	ENSP00000247986.2	Q9P2E2-1
	KIF17	ENST00000375044.5	TSL:1	c.2493+1414C>G		intron	N/A	ENSP00000364184.1	A0A0A0MRS8

Frequencies

GnomAD3 genomes AF: 0.0116 AC: 1758 AN: 152024 Hom.: 36 Cov.: 31

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00517

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0116 AC: 1767 AN: 152146 Hom.: 37 Cov.: 31 AF XY: 0.0110 AC XY: 819 AN XY: 74386

African (AFR) AF: 0.0398 AC: 1654 AN: 41524

American (AMR) AF: 0.00517 AC: 79 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5140

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 67998

Other (OTH) AF: 0.0118 AC: 25 AN: 2110

Alfa AF: 0.00680 Hom.: 1

Bravo AF: 0.0131

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism

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: rs6677104; hg19: chr1-20995500; COSMIC: COSV56117891; COSMIC: COSV56117891;