rs957957

Variant names:

• chr1-201018670-G-A
• rs957957
• NM_001252102.2:c.41+4673C>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.41+4673C>T 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 152,048 control chromosomes in the GnomAD database, including 26,173 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 (26173 hom., cov: 32)
• Consequence: KIF21B NM_001252102.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 9 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 = 0.828 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.41+4673C>T		intron	N/A	NP_001239031.1	O75037-4
	KIF21B	NM_001252100.2		c.41+4673C>T		intron	N/A	NP_001239029.1	O75037-1
	KIF21B	NM_017596.4		c.41+4673C>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.41+4673C>T		intron	N/A	ENSP00000433808.1	O75037-4
	KIF21B	ENST00000422435.2	TSL:1	c.41+4673C>T		intron	N/A	ENSP00000411831.2	O75037-1
	KIF21B	ENST00000332129.6	TSL:1	c.41+4673C>T		intron	N/A	ENSP00000328494.2	O75037-2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84918 AN: 151930 Hom.: 26119 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.559 AC: 85029 AN: 152048 Hom.: 26173 Cov.: 32 AF XY: 0.551 AC XY: 40959 AN XY: 74318

African (AFR) AF: 0.836 AC: 34673 AN: 41494

American (AMR) AF: 0.426 AC: 6503 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2352 AN: 5178

South Asian (SAS) AF: 0.337 AC: 1622 AN: 4810

European-Finnish (FIN) AF: 0.441 AC: 4654 AN: 10546

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31973 AN: 67956

Other (OTH) AF: 0.510 AC: 1078 AN: 2114

Alfa AF: 0.480 Hom.: 9490

Bravo AF: 0.574

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.21
PhyloP100		-0.51
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: rs957957; hg19: chr1-200987798;