rs12089839

Variant names:

• chr1-200997894-G-A
• rs12089839
• NM_001252102.2:c.2077+490C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-200997894-G-A
• chr1-200997894-G-T

Variant summary

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

The NM_001252102.2(KIF21B):​c.2077+490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,218 control chromosomes in the GnomAD database, including 297 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 0.043 (297 hom., cov: 33)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 2 publications found

Genes affected

KIF21B (HGNC:29442): (kinesin family member 21B) This gene encodes a member of the kinesin superfamily. Kinesins are ATP-dependent microtubule-based motor proteins that are involved in the intracellular transport of membranous organelles. Single nucleotide polymorphisms in this gene are associated with inflammatory bowel disease and multiple sclerosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001252102.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	NM_001252102.2	MANE Select	c.2077+490C>T		intron	N/A	NP_001239031.1
	KIF21B	NM_001252100.2		c.2077+490C>T		intron	N/A	NP_001239029.1
	KIF21B	NM_017596.4		c.2077+490C>T		intron	N/A	NP_060066.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	ENST00000461742.7	TSL:1 MANE Select	c.2077+490C>T		intron	N/A	ENSP00000433808.1
	KIF21B	ENST00000422435.2	TSL:1	c.2077+490C>T		intron	N/A	ENSP00000411831.2
	KIF21B	ENST00000332129.6	TSL:1	c.2077+490C>T		intron	N/A	ENSP00000328494.2

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 6556 AN: 152100 Hom.: 294 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00297

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0433 AC: 6587 AN: 152218 Hom.: 297 Cov.: 33 AF XY: 0.0460 AC XY: 3426 AN XY: 74440

African (AFR) AF: 0.102 AC: 4229 AN: 41500

American (AMR) AF: 0.0574 AC: 878 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3470

East Asian (EAS) AF: 0.116 AC: 601 AN: 5180

South Asian (SAS) AF: 0.0692 AC: 334 AN: 4828

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00295 AC: 201 AN: 68026

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

Alfa AF: 0.0146 Hom.: 139

Bravo AF: 0.0492

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.77
PhyloP100		0.17
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: rs12089839; hg19: chr1-200967022;