rs3198583

Variant names:

• chr1-200971052-G-A
• rs3198583
• NM_001252102.2:c.*2469C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-200971052-G-A
• chr1-200971052-G-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.*2469C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,864 control chromosomes in the GnomAD database, including 6,867 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 0.28 (6841 hom., cov: 34)
  • Exomes 𝑓: 0.31 (26 hom.)
• Consequence: KIF21B NM_001252102.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	NM_001252102.2	MANE Select	c.*2469C>T		3_prime_UTR	Exon 35 of 35	NP_001239031.1	O75037-4
	KIF21B	NM_001252100.2		c.*3043C>T		3_prime_UTR	Exon 35 of 35	NP_001239029.1	O75037-1
	KIF21B	NM_017596.4		c.*3043C>T		3_prime_UTR	Exon 34 of 34	NP_060066.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	ENST00000461742.7	TSL:1 MANE Select	c.*2469C>T		3_prime_UTR	Exon 35 of 35	ENSP00000433808.1	O75037-4
	KIF21B	ENST00000332129.6	TSL:1	c.*3043C>T		3_prime_UTR	Exon 34 of 34	ENSP00000328494.2	O75037-2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42896 AN: 152120 Hom.: 6830 Cov.: 34

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.305 AC: 191 AN: 626 Hom.: 26 Cov.: 0 AF XY: 0.306 AC XY: 121 AN XY: 396

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.377 AC: 46 AN: 122

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.304 AC: 123 AN: 404

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.233 AC: 20 AN: 86

Other (OTH) AF: 0.167 AC: 2 AN: 12

GnomAD4 genome AF: 0.282 AC: 42913 AN: 152238 Hom.: 6841 Cov.: 34 AF XY: 0.288 AC XY: 21412 AN XY: 74422

African (AFR) AF: 0.135 AC: 5622 AN: 41564

American (AMR) AF: 0.387 AC: 5914 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1228 AN: 5172

South Asian (SAS) AF: 0.465 AC: 2247 AN: 4828

European-Finnish (FIN) AF: 0.329 AC: 3481 AN: 10592

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22227 AN: 67998

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.287 Hom.: 2692

Bravo AF: 0.277

Asia WGS AF: 0.310 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.70
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3198583; hg19: chr1-200940180; COSMIC: COSV59752148; COSMIC: COSV59752148;