rs736866

Variant names:

• chr17-44932429-C-A
• rs736866
• NM_001265577.2:c.1239-223G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-44932429-C-A
• chr17-44932429-C-G
• chr17-44932429-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001265577.2(KIF18B):​c.1239-223G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 599,624 control chromosomes in the GnomAD database, including 47,406 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.38 (10882 hom., cov: 32)
  • Exomes 𝑓: 0.40 (36524 hom.)
• Consequence: KIF18B NM_001265577.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 5 publications found

Genes affected

KIF18B (HGNC:27102): (kinesin family member 18B) Enables cytoskeletal motor activity and kinesin binding activity. Involved in microtubule depolymerization; mitotic cell cycle; and regulation of cell division. Located in cytosol; microtubule; and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF18B	NM_001265577.2	c.1239-223G>T		intron_variant	Intron 9 of 15	ENST00000593135.6	NP_001252506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF18B	ENST00000593135.6	c.1239-223G>T		intron_variant	Intron 9 of 15	5	NM_001265577.2	ENSP00000465992.1
KIF18B	ENST00000590129.1	c.1266-187G>T		intron_variant	Intron 8 of 13	1		ENSP00000465501.1
KIF18B	ENST00000585687.1	n.474G>T		non_coding_transcript_exon_variant	Exon 3 of 3	3
KIF18B	ENST00000587309.5	c.1239-187G>T		intron_variant	Intron 9 of 14	5		ENSP00000465377.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57350 AN: 151782 Hom.: 10864 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.376

GnomAD4 exome AF: 0.401 AC: 179738 AN: 447724 Hom.: 36524 Cov.: 5 AF XY: 0.401 AC XY: 93672 AN XY: 233348

African (AFR) AF: 0.325 AC: 4059 AN: 12500

American (AMR) AF: 0.371 AC: 6804 AN: 18316

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 6095 AN: 13488

East Asian (EAS) AF: 0.408 AC: 12582 AN: 30840

South Asian (SAS) AF: 0.403 AC: 16741 AN: 41494

European-Finnish (FIN) AF: 0.379 AC: 11190 AN: 29488

Middle Eastern (MID) AF: 0.393 AC: 758 AN: 1930

European-Non Finnish (NFE) AF: 0.407 AC: 111372 AN: 273806

Other (OTH) AF: 0.392 AC: 10137 AN: 25862

GnomAD4 genome AF: 0.378 AC: 57412 AN: 151900 Hom.: 10882 Cov.: 32 AF XY: 0.376 AC XY: 27886 AN XY: 74220

African (AFR) AF: 0.330 AC: 13641 AN: 41394

American (AMR) AF: 0.354 AC: 5412 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3470

East Asian (EAS) AF: 0.388 AC: 1997 AN: 5148

South Asian (SAS) AF: 0.392 AC: 1884 AN: 4812

European-Finnish (FIN) AF: 0.393 AC: 4142 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27432 AN: 67934

Other (OTH) AF: 0.375 AC: 792 AN: 2112

Alfa AF: 0.398 Hom.: 20432

Bravo AF: 0.373

Asia WGS AF: 0.370 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.69
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs736866; hg19: chr17-43009797;