rs10494828

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001252102.2(KIF21B):​c.3408+392C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,148 control chromosomes in the GnomAD database, including 4,061 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 0.22 ( 4061 hom., cov: 32)

Consequence

KIF21B
NM_001252102.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.849
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIF21BNM_001252102.2 linkc.3408+392C>T intron_variant Intron 24 of 34 ENST00000461742.7 NP_001239031.1 O75037-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIF21BENST00000461742.7 linkc.3408+392C>T intron_variant Intron 24 of 34 1 NM_001252102.2 ENSP00000433808.1 O75037-4
KIF21BENST00000422435.2 linkc.3408+392C>T intron_variant Intron 24 of 34 1 ENSP00000411831.2 O75037-1
KIF21BENST00000332129.6 linkc.3408+392C>T intron_variant Intron 24 of 33 1 ENSP00000328494.2 O75037-2
KIF21BENST00000360529.9 linkc.3408+392C>T intron_variant Intron 24 of 33 1 ENSP00000353724.5 O75037-3

Frequencies

GnomAD3 genomes
AF:
0.219
AC:
33353
AN:
152030
Hom.:
4059
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.173
Gnomad AMI
AF:
0.437
Gnomad AMR
AF:
0.163
Gnomad ASJ
AF:
0.219
Gnomad EAS
AF:
0.00385
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.204
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33357
AN:
152148
Hom.:
4061
Cov.:
32
AF XY:
0.212
AC XY:
15779
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.173
Gnomad4 AMR
AF:
0.163
Gnomad4 ASJ
AF:
0.219
Gnomad4 EAS
AF:
0.00386
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.204
Gnomad4 NFE
AF:
0.284
Gnomad4 OTH
AF:
0.206
Alfa
AF:
0.261
Hom.:
5348
Bravo
AF:
0.216
Asia WGS
AF:
0.0660
AC:
233
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
0.11
DANN
Benign
0.38

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10494828; hg19: chr1-200957032; API