6-33409703-ATC-ATCTCTCTC

Variant names:

• chr6-33409703-A-ATCTCTC
• rs752059822
• NM_002263.4:c.*16_*17insCTCTCT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_002263.4(KIFC1):​c.*16_*17insCTCTCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000345 in 86,878 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000035 (0 hom., cov: 28)
  • Exomes 𝑓: 0.0000088 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KIFC1 NM_002263.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 0 publications found

Genes affected

KIFC1 (HGNC:6389): (kinesin family member C1) Predicted to enable microtubule binding activity and minus-end-directed microtubule motor activity. Involved in mitotic metaphase plate congression and mitotic spindle assembly. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002263.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIFC1	NM_002263.4	MANE Select	c.*16_*17insCTCTCT		3_prime_UTR	Exon 11 of 11	NP_002254.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIFC1	ENST00000428849.7	TSL:1 MANE Select	c.*16_*17insCTCTCT		3_prime_UTR	Exon 11 of 11	ENSP00000393963.2

Frequencies

GnomAD3 genomes AF: 0.0000345 AC: 3 AN: 86878 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000456

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000238

Gnomad OTH AF: 0.000885

GnomAD2 exomes AF: 0.0000104 AC: 2 AN: 192512 AF XY: 0.0000191

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000883 AC: 11 AN: 1245658 Hom.: 0 Cov.: 34 AF XY: 0.0000128 AC XY: 8 AN XY: 624210

African (AFR) AF: 0.00 AC: 0 AN: 30222

American (AMR) AF: 0.00 AC: 0 AN: 39878

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22386

East Asian (EAS) AF: 0.00 AC: 0 AN: 33960

South Asian (SAS) AF: 0.000101 AC: 8 AN: 79228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38116

Middle Eastern (MID) AF: 0.000500 AC: 2 AN: 4000

European-Non Finnish (NFE) AF: 0.00000106 AC: 1 AN: 946528

Other (OTH) AF: 0.00 AC: 0 AN: 51340

GnomAD4 genome AF: 0.0000345 AC: 3 AN: 86878 Hom.: 0 Cov.: 28 AF XY: 0.0000243 AC XY: 1 AN XY: 41206

African (AFR) AF: 0.00 AC: 0 AN: 23798

American (AMR) AF: 0.00 AC: 0 AN: 7930

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1994

East Asian (EAS) AF: 0.00 AC: 0 AN: 2718

South Asian (SAS) AF: 0.000456 AC: 1 AN: 2192

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4242

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 178

European-Non Finnish (NFE) AF: 0.0000238 AC: 1 AN: 42014

Other (OTH) AF: 0.000885 AC: 1 AN: 1130

Alfa AF: 0.00 Hom.: 430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs752059822; hg19: chr6-33377480;