1-200980241-A-T

Variant names:

• chr1-200980241-A-T
• rs296560
• NM_001252102.2:c.3980-526T>A

Variant summary

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

The NM_001252102.2(KIF21B):​c.3980-526T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,266 control chromosomes in the GnomAD database, including 68,919 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 0.95 (68919 hom., cov: 32)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 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.3980-526T>A		intron	N/A	NP_001239031.1
	KIF21B	NM_001252100.2		c.3980-526T>A		intron	N/A	NP_001239029.1
	KIF21B	NM_017596.4		c.3941-526T>A		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.3980-526T>A		intron	N/A	ENSP00000433808.1
	KIF21B	ENST00000422435.2	TSL:1	c.3980-526T>A		intron	N/A	ENSP00000411831.2
	KIF21B	ENST00000332129.6	TSL:1	c.3941-526T>A		intron	N/A	ENSP00000328494.2

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144626 AN: 152148 Hom.: 68884 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.950 AC: 144713 AN: 152266 Hom.: 68919 Cov.: 32 AF XY: 0.948 AC XY: 70545 AN XY: 74450

African (AFR) AF: 0.933 AC: 38785 AN: 41556

American (AMR) AF: 0.953 AC: 14585 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3304 AN: 3470

East Asian (EAS) AF: 0.791 AC: 4092 AN: 5172

South Asian (SAS) AF: 0.910 AC: 4388 AN: 4820

European-Finnish (FIN) AF: 0.941 AC: 9981 AN: 10608

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66409 AN: 68018

Other (OTH) AF: 0.938 AC: 1984 AN: 2116

Alfa AF: 0.961 Hom.: 8725

Bravo AF: 0.950

Asia WGS AF: 0.837 AC: 2910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.23
PhyloP100		-0.74
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: rs296560; hg19: chr1-200949369;