6-33409703-ATC-ATCTCTC

Variant names:

• chr6-33409703-A-ATCTC
• rs752059822
• NM_002263.4:c.*16_*17insCTCT

Variant summary

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

The ENST00000428849.7(KIFC1):​c.*16_*17insCTCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,330,950 control chromosomes in the GnomAD database, including 43 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0074 (10 hom., cov: 28)
  • Exomes 𝑓: 0.0015 (33 hom.)
• Consequence: KIFC1 ENST00000428849.7 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 647 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428849.7. 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_*17insCTCT		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_*17insCTCT		3_prime_UTR	Exon 11 of 11	ENSP00000393963.2

Frequencies

GnomAD3 genomes AF: 0.00745 AC: 647 AN: 86866 Hom.: 10 Cov.: 28

Gnomad AFR AF: 0.00273

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.00530

Gnomad ASJ AF: 0.00752

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000912

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00728

Gnomad OTH AF: 0.00531

GnomAD2 exomes AF: 0.00133 AC: 256 AN: 192512 AF XY: 0.00139

Gnomad AFR exome AF: 0.000635

Gnomad AMR exome AF: 0.000458

Gnomad ASJ exome AF: 0.000605

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00876

Gnomad NFE exome AF: 0.00138

Gnomad OTH exome AF: 0.00101

GnomAD4 exome AF: 0.00152 AC: 1893 AN: 1243992 Hom.: 33 Cov.: 34 AF XY: 0.00149 AC XY: 931 AN XY: 623316

African (AFR) AF: 0.000397 AC: 12 AN: 30202

American (AMR) AF: 0.000578 AC: 23 AN: 39824

Ashkenazi Jewish (ASJ) AF: 0.00121 AC: 27 AN: 22346

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

South Asian (SAS) AF: 0.000682 AC: 54 AN: 79150

European-Finnish (FIN) AF: 0.0122 AC: 461 AN: 37694

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4000

European-Non Finnish (NFE) AF: 0.00132 AC: 1249 AN: 945572

Other (OTH) AF: 0.00131 AC: 67 AN: 51244

GnomAD4 genome AF: 0.00744 AC: 647 AN: 86958 Hom.: 10 Cov.: 28 AF XY: 0.00838 AC XY: 346 AN XY: 41290

African (AFR) AF: 0.00272 AC: 65 AN: 23876

American (AMR) AF: 0.00529 AC: 42 AN: 7936

Ashkenazi Jewish (ASJ) AF: 0.00752 AC: 15 AN: 1994

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

South Asian (SAS) AF: 0.000906 AC: 2 AN: 2208

European-Finnish (FIN) AF: 0.0470 AC: 199 AN: 4236

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 166

European-Non Finnish (NFE) AF: 0.00728 AC: 306 AN: 42008

Other (OTH) AF: 0.00529 AC: 6 AN: 1134

Alfa AF: 0.00117 Hom.: 430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism

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;