rs3738255

Variant names:

• chr1-200972588-G-A
• rs3738255
• NM_001252102.2:c.*933C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-200972588-G-A
• chr1-200972588-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001252102.2(KIF21B):​c.*933C>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 0.276 in 152,716 control chromosomes in the GnomAD database, including 6,583 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 (6560 hom., cov: 33)
  • Exomes 𝑓: 0.29 (23 hom.)
• Consequence: KIF21B NM_001252102.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF21B	NM_001252102.2	c.*933C>T		3_prime_UTR_variant	Exon 35 of 35	ENST00000461742.7	NP_001239031.1
KIF21B	NM_001252100.2	c.*1507C>T		3_prime_UTR_variant	Exon 35 of 35		NP_001239029.1
KIF21B	NM_017596.4	c.*1507C>T		3_prime_UTR_variant	Exon 34 of 34		NP_060066.2
KIF21B	NM_001252103.2	c.*933C>T		3_prime_UTR_variant	Exon 34 of 34		NP_001239032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF21B	ENST00000461742	c.*933C>T		3_prime_UTR_variant	Exon 35 of 35	1	NM_001252102.2	ENSP00000433808.1
KIF21B	ENST00000332129	c.*1507C>T		3_prime_UTR_variant	Exon 34 of 34	1		ENSP00000328494.2

Frequencies

GnomAD3 genomes AF: 0.276 AC: 42017 AN: 152006 Hom.: 6549 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.285 AC: 169 AN: 592 Hom.: 23 Cov.: 0 AF XY: 0.276 AC XY: 102 AN XY: 370

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.261

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.276 AC: 42033 AN: 152124 Hom.: 6560 Cov.: 33 AF XY: 0.282 AC XY: 20995 AN XY: 74372

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.309

Alfa AF: 0.210 Hom.: 587

Bravo AF: 0.272

Asia WGS AF: 0.310 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738255; hg19: chr1-200941716;