chr6-33409703-A-ATCTC

Position:

• chr6-33409703-A-ATCTC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_002263.4(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 NM_002263.4 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 Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

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

Ensembl

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

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

GnomAD3 exomes AF: 0.00133 AC: 256 AN: 192512 Hom.: 4 AF XY: 0.00139 AC XY: 146 AN XY: 104726

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 SAS exome AF: 0.000643

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

Gnomad4 AFR exome AF: 0.000397

Gnomad4 AMR exome AF: 0.000578

Gnomad4 ASJ exome AF: 0.00121

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000682

Gnomad4 FIN exome AF: 0.0122

Gnomad4 NFE exome AF: 0.00132

Gnomad4 OTH exome AF: 0.00131

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

Gnomad4 AFR AF: 0.00272

Gnomad4 AMR AF: 0.00529

Gnomad4 ASJ AF: 0.00752

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000906

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.00728

Gnomad4 OTH AF: 0.00529

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;