chr15-69414437-C-T

Variant names:

• chr15-69414437-C-T
• rs62007332
• NM_001367805.3:c.-29C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001367805.3(KIF23):​c.-29C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,581,124 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0027 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0041 (16 hom.)
• Consequence: KIF23 NM_001367805.3 5_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0700
• Publications: 2 publications found

Genes affected

KIF23 (HGNC:6392): (kinesin family member 23) The protein encoded by this gene is a member of kinesin-like protein family. This family includes microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. This protein has been shown to cross-bridge antiparallel microtubules and drive microtubule movement in vitro. Alternate splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2013]

KIF23-AS1 (HGNC:27075): (KIF23 and PAQR5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS2: High AC in GnomAd4 at 414 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367805.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF23	NM_001367805.3	MANE Select	c.-29C>T		5_prime_UTR	Exon 1 of 24	NP_001354734.1	A0A7I2V5Y5
	KIF23	NM_138555.4		c.-29C>T		5_prime_UTR	Exon 1 of 23	NP_612565.1	Q02241-1
	KIF23	NM_001367804.2		c.-29C>T		5_prime_UTR	Exon 1 of 22	NP_001354733.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF23	ENST00000679126.1	MANE Select	c.-29C>T		5_prime_UTR	Exon 1 of 24	ENSP00000504770.1	A0A7I2V5Y5
	KIF23	ENST00000260363.9	TSL:1	c.-29C>T		5_prime_UTR	Exon 1 of 23	ENSP00000260363.4	Q02241-1
	KIF23	ENST00000352331.8	TSL:1	c.-29C>T		5_prime_UTR	Exon 1 of 22	ENSP00000304978.6	Q02241-2

Frequencies

GnomAD3 genomes AF: 0.00272 AC: 414 AN: 152250 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.000941

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00222

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00479

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00219 AC: 421 AN: 192398 AF XY: 0.00219

Gnomad AFR exome AF: 0.000920

Gnomad AMR exome AF: 0.00125

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000465

Gnomad NFE exome AF: 0.00411

Gnomad OTH exome AF: 0.00184

GnomAD4 exome AF: 0.00413 AC: 5894 AN: 1428756 Hom.: 16 Cov.: 30 AF XY: 0.00400 AC XY: 2828 AN XY: 707698

African (AFR) AF: 0.000457 AC: 15 AN: 32854

American (AMR) AF: 0.00132 AC: 53 AN: 40188

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25490

East Asian (EAS) AF: 0.00 AC: 0 AN: 38072

South Asian (SAS) AF: 0.000898 AC: 73 AN: 81298

European-Finnish (FIN) AF: 0.000417 AC: 21 AN: 50414

Middle Eastern (MID) AF: 0.000707 AC: 4 AN: 5654

European-Non Finnish (NFE) AF: 0.00503 AC: 5508 AN: 1095766

Other (OTH) AF: 0.00373 AC: 220 AN: 59020

GnomAD4 genome AF: 0.00272 AC: 414 AN: 152368 Hom.: 3 Cov.: 33 AF XY: 0.00235 AC XY: 175 AN XY: 74504

African (AFR) AF: 0.000938 AC: 39 AN: 41584

American (AMR) AF: 0.00222 AC: 34 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000828 AC: 4 AN: 4832

European-Finnish (FIN) AF: 0.000471 AC: 5 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00479 AC: 326 AN: 68034

Other (OTH) AF: 0.00284 AC: 6 AN: 2116

Alfa AF: 0.00244 Hom.: 0

Bravo AF: 0.00276

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.6
DANN	Benign	0.88
PhyloP100		0.070
PromoterAI		-0.30	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=296/4	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs62007332; hg19: chr15-69706776;