chr1-201011570-A-G

Variant names:

• chr1-201011570-A-G
• rs6687260
• NM_001252102.2:c.42-2082T>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.42-2082T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,214 control chromosomes in the GnomAD database, including 26,119 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 0.56 (26119 hom., cov: 34)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF21B	NM_001252102.2	c.42-2082T>C		intron_variant	Intron 1 of 34	ENST00000461742.7	NP_001239031.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF21B	ENST00000461742.7	c.42-2082T>C		intron_variant	Intron 1 of 34	1	NM_001252102.2	ENSP00000433808.1
KIF21B	ENST00000422435.2	c.42-2082T>C		intron_variant	Intron 1 of 34	1		ENSP00000411831.2
KIF21B	ENST00000332129.6	c.42-2082T>C		intron_variant	Intron 1 of 33	1		ENSP00000328494.2
KIF21B	ENST00000360529.9	c.42-2082T>C		intron_variant	Intron 1 of 33	1		ENSP00000353724.5

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84921 AN: 152096 Hom.: 26064 Cov.: 34

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.559 AC: 85033 AN: 152214 Hom.: 26119 Cov.: 34 AF XY: 0.551 AC XY: 40977 AN XY: 74404

African (AFR) AF: 0.833 AC: 34593 AN: 41538

American (AMR) AF: 0.425 AC: 6494 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2342 AN: 5168

South Asian (SAS) AF: 0.342 AC: 1651 AN: 4832

European-Finnish (FIN) AF: 0.442 AC: 4679 AN: 10594

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32028 AN: 68004

Other (OTH) AF: 0.509 AC: 1075 AN: 2112

Alfa AF: 0.498 Hom.: 3321

Bravo AF: 0.574

Asia WGS AF: 0.463 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.37
PhyloP100		-0.44
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: rs6687260; hg19: chr1-200980698;