NM_001252102.2:c.*1226G>T

Variant names:

• chr1-200972295-C-A
• rs56368827
• NM_001252102.2:c.*1226G>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.*1226G>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 0.255 in 152,110 control chromosomes in the GnomAD database, including 5,836 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 0.25 (5833 hom., cov: 32)
  • Exomes 𝑓: 0.19 (3 hom.)
• Consequence: KIF21B NM_001252102.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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.*1226G>T		3_prime_UTR	Exon 35 of 35	NP_001239031.1
	KIF21B	NM_001252100.2		c.*1800G>T		3_prime_UTR	Exon 35 of 35	NP_001239029.1
	KIF21B	NM_017596.4		c.*1800G>T		3_prime_UTR	Exon 34 of 34	NP_060066.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	ENST00000461742.7	TSL:1 MANE Select	c.*1226G>T		3_prime_UTR	Exon 35 of 35	ENSP00000433808.1
	KIF21B	ENST00000332129.6	TSL:1	c.*1800G>T		3_prime_UTR	Exon 34 of 34	ENSP00000328494.2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38680 AN: 151802 Hom.: 5835 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.191 AC: 36 AN: 188 Hom.: 3 Cov.: 0 AF XY: 0.203 AC XY: 24 AN XY: 118

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.201 AC: 27 AN: 134

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.159 AC: 7 AN: 44

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.255 AC: 38693 AN: 151922 Hom.: 5833 Cov.: 32 AF XY: 0.253 AC XY: 18811 AN XY: 74218

African (AFR) AF: 0.416 AC: 17230 AN: 41442

American (AMR) AF: 0.203 AC: 3109 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.300 AC: 1543 AN: 5144

South Asian (SAS) AF: 0.115 AC: 552 AN: 4814

European-Finnish (FIN) AF: 0.247 AC: 2607 AN: 10556

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12370 AN: 67894

Other (OTH) AF: 0.230 AC: 484 AN: 2108

Alfa AF: 0.218 Hom.: 860

Bravo AF: 0.259

Asia WGS AF: 0.218 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		0.16
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: rs56368827; hg19: chr1-200941423;