1-200972588-G-A

Variant names:

• chr1-200972588-G-A
• rs3738255
• NM_001252102.2:c.*933C>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.*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
• Publications: 10 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=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 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.*933C>T		3_prime_UTR	Exon 35 of 35	NP_001239031.1	O75037-4
	KIF21B	NM_001252100.2		c.*1507C>T		3_prime_UTR	Exon 35 of 35	NP_001239029.1	O75037-1
	KIF21B	NM_017596.4		c.*1507C>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.*933C>T		3_prime_UTR	Exon 35 of 35	ENSP00000433808.1	O75037-4
	KIF21B	ENST00000332129.6	TSL:1	c.*1507C>T		3_prime_UTR	Exon 34 of 34	ENSP00000328494.2	O75037-2

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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.167 AC: 1 AN: 6

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.300 AC: 126 AN: 420

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.261 AC: 37 AN: 142

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

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

African (AFR) AF: 0.134 AC: 5554 AN: 41550

American (AMR) AF: 0.383 AC: 5858 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1231 AN: 5152

South Asian (SAS) AF: 0.459 AC: 2220 AN: 4832

European-Finnish (FIN) AF: 0.324 AC: 3429 AN: 10590

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21574 AN: 67912

Other (OTH) AF: 0.309 AC: 651 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.91
PhyloP100		0.41
Mutation Taster		=98/2	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3738255;

hg19: chr1-200941716;