rs56368827

Positions:

• chr1-200972295-C-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF21B	NM_001252102.2	c.*1226G>T		3_prime_UTR_variant	35/35	ENST00000461742.7	NP_001239031.1
KIF21B	NM_001252100.2	c.*1800G>T		3_prime_UTR_variant	35/35		NP_001239029.1
KIF21B	NM_001252103.2	c.*1226G>T		3_prime_UTR_variant	34/34		NP_001239032.1
KIF21B	NM_017596.4	c.*1800G>T		3_prime_UTR_variant	34/34		NP_060066.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF21B	ENST00000461742.7	c.*1226G>T		3_prime_UTR_variant	35/35	1	NM_001252102.2	ENSP00000433808	P3
KIF21B	ENST00000332129.6	c.*1800G>T		3_prime_UTR_variant	34/34	1		ENSP00000328494

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

Gnomad4 EAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.159

Gnomad4 OTH exome AF: 0.250

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

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.230

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56368827; hg19: chr1-200941423;