chr1-200983327-A-G

Variant names:

• chr1-200983327-A-G
• rs12568529
• NM_001252102.2:c.3804-233T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001252102.2(KIF21B):​c.3804-233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,952 control chromosomes in the GnomAD database, including 6,086 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 0.26 (6086 hom., cov: 32)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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.3804-233T>C		intron	N/A	NP_001239031.1
	KIF21B	NM_001252100.2		c.3804-233T>C		intron	N/A	NP_001239029.1
	KIF21B	NM_017596.4		c.3803+1532T>C		intron	N/A	NP_060066.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	ENST00000461742.7	TSL:1 MANE Select	c.3804-233T>C		intron	N/A	ENSP00000433808.1
	KIF21B	ENST00000422435.2	TSL:1	c.3804-233T>C		intron	N/A	ENSP00000411831.2
	KIF21B	ENST00000332129.6	TSL:1	c.3803+1532T>C		intron	N/A	ENSP00000328494.2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39184 AN: 151834 Hom.: 6083 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.258 AC: 39210 AN: 151952 Hom.: 6086 Cov.: 32 AF XY: 0.257 AC XY: 19059 AN XY: 74294

African (AFR) AF: 0.431 AC: 17840 AN: 41402

American (AMR) AF: 0.206 AC: 3152 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1537 AN: 5140

South Asian (SAS) AF: 0.114 AC: 550 AN: 4816

European-Finnish (FIN) AF: 0.235 AC: 2489 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12358 AN: 67938

Other (OTH) AF: 0.231 AC: 488 AN: 2108

Alfa AF: 0.225 Hom.: 572

Bravo AF: 0.264

Asia WGS AF: 0.221 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.26
PhyloP100		-0.078
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: rs12568529; hg19: chr1-200952455; COSMIC: COSV59765115;