chr1-201015352-G-A

Variant names:

• chr1-201015352-G-A
• rs12122721
• NM_001252102.2:c.42-5864C>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.42-5864C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,106 control chromosomes in the GnomAD database, including 4,506 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 0.24 (4506 hom., cov: 33)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 25 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 = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF21B	NM_001252102.2	c.42-5864C>T		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.42-5864C>T		intron_variant	Intron 1 of 34	1	NM_001252102.2	ENSP00000433808.1
KIF21B	ENST00000422435.2	c.42-5864C>T		intron_variant	Intron 1 of 34	1		ENSP00000411831.2
KIF21B	ENST00000332129.6	c.42-5864C>T		intron_variant	Intron 1 of 33	1		ENSP00000328494.2
KIF21B	ENST00000360529.9	c.42-5864C>T		intron_variant	Intron 1 of 33	1		ENSP00000353724.5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36208 AN: 151988 Hom.: 4492 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.238 AC: 36256 AN: 152106 Hom.: 4506 Cov.: 33 AF XY: 0.235 AC XY: 17460 AN XY: 74366

African (AFR) AF: 0.190 AC: 7880 AN: 41490

American (AMR) AF: 0.208 AC: 3184 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3468

East Asian (EAS) AF: 0.119 AC: 617 AN: 5184

South Asian (SAS) AF: 0.178 AC: 856 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2426 AN: 10574

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19548 AN: 67968

Other (OTH) AF: 0.231 AC: 485 AN: 2104

Alfa AF: 0.266 Hom.: 9441

Bravo AF: 0.236

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.087
DANN	Benign	0.34
PhyloP100		-1.8
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: rs12122721; hg19: chr1-200984480;