rs12087649

Variant names:

• chr1-200982312-T-A
• rs12087649
• NM_001252102.2:c.3842+744A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-200982312-T-A
• chr1-200982312-T-C

Variant summary

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

The NM_001252102.2(KIF21B):​c.3842+744A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,034 control chromosomes in the GnomAD database, including 10,049 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 0.32 (10049 hom., cov: 32)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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.3842+744A>T		intron	N/A	NP_001239031.1
	KIF21B	NM_001252100.2		c.3842+744A>T		intron	N/A	NP_001239029.1
	KIF21B	NM_017596.4		c.3804-1216A>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.3842+744A>T		intron	N/A	ENSP00000433808.1
	KIF21B	ENST00000422435.2	TSL:1	c.3842+744A>T		intron	N/A	ENSP00000411831.2
	KIF21B	ENST00000332129.6	TSL:1	c.3804-1216A>T		intron	N/A	ENSP00000328494.2

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48133 AN: 151916 Hom.: 10025 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.317 AC: 48201 AN: 152034 Hom.: 10049 Cov.: 32 AF XY: 0.317 AC XY: 23556 AN XY: 74302

African (AFR) AF: 0.585 AC: 24252 AN: 41474

American (AMR) AF: 0.270 AC: 4130 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3462

East Asian (EAS) AF: 0.424 AC: 2181 AN: 5144

South Asian (SAS) AF: 0.186 AC: 895 AN: 4806

European-Finnish (FIN) AF: 0.260 AC: 2751 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12597 AN: 67956

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.156 Hom.: 352

Bravo AF: 0.332

Asia WGS AF: 0.336 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.79
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: rs12087649; hg19: chr1-200951440;