17-44930583-T-C

Variant names:

• chr17-44930583-T-C
• rs9908100
• NM_001265577.2:c.1517+1019A>G

Variant summary

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

The NM_001265577.2(KIF18B):​c.1517+1019A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,070 control chromosomes in the GnomAD database, including 3,459 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 0.21 (3459 hom., cov: 32)
• Consequence: KIF18B NM_001265577.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF18B	NM_001265577.2	c.1517+1019A>G		intron_variant	Intron 11 of 15	ENST00000593135.6	NP_001252506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF18B	ENST00000593135.6	c.1517+1019A>G		intron_variant	Intron 11 of 15	5	NM_001265577.2	ENSP00000465992.1
KIF18B	ENST00000590129.1	c.1580+1019A>G		intron_variant	Intron 10 of 13	1		ENSP00000465501.1
KIF18B	ENST00000587309.5	c.1553+1019A>G		intron_variant	Intron 11 of 14	5		ENSP00000465377.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31887 AN: 151952 Hom.: 3443 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.195

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.210 AC: 31935 AN: 152070 Hom.: 3459 Cov.: 32 AF XY: 0.213 AC XY: 15841 AN XY: 74354

African (AFR) AF: 0.171 AC: 7101 AN: 41482

American (AMR) AF: 0.228 AC: 3489 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3464

East Asian (EAS) AF: 0.374 AC: 1935 AN: 5174

South Asian (SAS) AF: 0.202 AC: 975 AN: 4816

European-Finnish (FIN) AF: 0.265 AC: 2800 AN: 10580

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14241 AN: 67968

Other (OTH) AF: 0.197 AC: 414 AN: 2104

Alfa AF: 0.212 Hom.: 13432

Bravo AF: 0.208

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs9908100; hg19: chr17-43007951;