6-33409703-ATC-ATCTCTCTC

Position:

• chr6-33409703-ATC-ATCTCTCTC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000428849.7(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 ENST00000428849.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIFC1	NM_002263.4	c.*16_*17insCTCTCT		3_prime_UTR_variant	11/11	ENST00000428849.7	NP_002254.2
KIFC1	XM_011514585.2	c.*101_*102insCTCTCT		3_prime_UTR_variant	12/12		XP_011512887.1
KIFC1	XM_011514587.3	c.*16_*17insCTCTCT		3_prime_UTR_variant	10/10		XP_011512889.1
KIFC1	XM_017010837.2	c.*16_*17insCTCTCT		3_prime_UTR_variant	11/11		XP_016866326.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIFC1	ENST00000428849.7	c.*16_*17insCTCTCT		3_prime_UTR_variant	11/11	1	NM_002263.4	ENSP00000393963	P1

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

GnomAD3 exomes AF: 0.0000104 AC: 2 AN: 192512 Hom.: 0 AF XY: 0.0000191 AC XY: 2 AN XY: 104726

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 SAS exome AF: 0.0000804

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000101

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000106

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000456

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000238

Gnomad4 OTH AF: 0.000885

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752059822; hg19: chr6-33377480;