rs752059822

Variant names:

• chr6-33409703-ATC-A
• rs752059822
• NM_002263.4:c.*15_*16delCT

Your query was ambiguous. Multiple possible variants found:

• chr6-33409703-ATC-A
• chr6-33409703-ATC-ATCTC
• chr6-33409703-ATC-ATCTCTC
• chr6-33409703-ATC-ATCTCTCTC
• chr6-33409703-ATC-ATCTCTGTC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_002263.4(KIFC1):​c.*15_*16delCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000976 in 1,332,554 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 0.000092 (0 hom., cov: 15)
  • Exomes 𝑓: 0.0000040 (0 hom.)
• Consequence: KIFC1 NM_002263.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 8 AD gene.

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.*15_*16delCT		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.*15_*16delCT		3_prime_UTR	Exon 11 of 11	ENSP00000393963.2

Frequencies

GnomAD3 genomes AF: 0.0000921 AC: 8 AN: 86878 Hom.: 0 Cov.: 15

Gnomad AFR AF: 0.000336

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000401 AC: 5 AN: 1245676 Hom.: 0 AF XY: 0.00000481 AC XY: 3 AN XY: 624224

African (AFR) AF: 0.0000662 AC: 2 AN: 30224

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: 0.00 AC: 0 AN: 79234

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4004

European-Non Finnish (NFE) AF: 0.00000211 AC: 2 AN: 946534

Other (OTH) AF: 0.0000195 AC: 1 AN: 51340

GnomAD4 genome AF: 0.0000921 AC: 8 AN: 86878 Hom.: 0 Cov.: 15 AF XY: 0.0000728 AC XY: 3 AN XY: 41206

African (AFR) AF: 0.000336 AC: 8 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: 0.00 AC: 0 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: 0.00 AC: 0 AN: 42014

Other (OTH) AF: 0.00 AC: 0 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		-0.29

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: rs752059822; hg19: chr6-33377480;