1-200997855-G-A

Variant names:

• chr1-200997855-G-A
• rs7536000
• NM_001252102.2:c.2077+529C>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.2077+529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,928 control chromosomes in the GnomAD database, including 27,892 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 0.59 (27892 hom., cov: 33)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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.2077+529C>T		intron	N/A	NP_001239031.1	O75037-4
	KIF21B	NM_001252100.2		c.2077+529C>T		intron	N/A	NP_001239029.1	O75037-1
	KIF21B	NM_017596.4		c.2077+529C>T		intron	N/A	NP_060066.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	ENST00000461742.7	TSL:1 MANE Select	c.2077+529C>T		intron	N/A	ENSP00000433808.1	O75037-4
	KIF21B	ENST00000422435.2	TSL:1	c.2077+529C>T		intron	N/A	ENSP00000411831.2	O75037-1
	KIF21B	ENST00000332129.6	TSL:1	c.2077+529C>T		intron	N/A	ENSP00000328494.2	O75037-2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88902 AN: 151808 Hom.: 27838 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.536

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.586 AC: 89011 AN: 151928 Hom.: 27892 Cov.: 33 AF XY: 0.582 AC XY: 43225 AN XY: 74264

African (AFR) AF: 0.824 AC: 34161 AN: 41458

American (AMR) AF: 0.482 AC: 7366 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1546 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3275 AN: 5168

South Asian (SAS) AF: 0.382 AC: 1845 AN: 4828

European-Finnish (FIN) AF: 0.522 AC: 5488 AN: 10504

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33502 AN: 67922

Other (OTH) AF: 0.542 AC: 1142 AN: 2108

Alfa AF: 0.544 Hom.: 2805

Bravo AF: 0.597

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.52
PhyloP100		-3.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7536000; hg19: chr1-200966983;