Genetic Variant KIF21B:c.*2469C>T (chr1-200971052-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001252102.2(KIF21B):c.*2469C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,864 control chromosomes in the GnomAD database, including 6,867 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 0.28 ( 6841 hom., cov: 34)

Exomes 𝑓: 0.31 ( 26 hom. )

Consequence

KIF21B
NM_001252102.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

Publications

14 publications found

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]

KIF21B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIF21B	NM_001252102.2	MANE Select	c.*2469C>T	3_prime_UTR	Exon 35 of 35	NP_001239031.1	O75037-4
KIF21B	NM_001252100.2		c.*3043C>T	3_prime_UTR	Exon 35 of 35	NP_001239029.1	O75037-1
KIF21B	NM_017596.4		c.*3043C>T	3_prime_UTR	Exon 34 of 34	NP_060066.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF21B	ENST00000461742.7	TSL:1 MANE Select	c.*2469C>T		3_prime_UTR	Exon 35 of 35	ENSP00000433808.1	O75037-4
	KIF21B	ENST00000332129.6	TSL:1	c.*3043C>T		3_prime_UTR	Exon 34 of 34	ENSP00000328494.2	O75037-2

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42896

AN:

152120

Hom.:

6830

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.465

Gnomad FIN

AF:

0.329

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.319

GnomAD4 exome

AF:

0.305

AC:

191

AN:

626

Hom.:

Cov.:

AF XY:

0.306

AC XY:

121

AN XY:

396

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.377

AC:

AN:

122

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.304

AC:

123

AN:

404

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.233

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.282

AC:

42913

AN:

152238

Hom.:

6841

Cov.:

AF XY:

0.288

AC XY:

21412

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.135

AC:

5622

AN:

41564

American (AMR)

AF:

0.387

AC:

5914

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

1265

AN:

3470

East Asian (EAS)

AF:

0.237

AC:

1228

AN:

5172

South Asian (SAS)

AF:

0.465

AC:

2247

AN:

4828

European-Finnish (FIN)

AF:

0.329

AC:

3481

AN:

10592

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.327

AC:

22227

AN:

67998

Other (OTH)

AF:

0.314

AC:

663

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1616

3232

4849

6465

8081

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.287

Hom.:

2692

Bravo

AF:

0.277

Asia WGS

AF:

0.310

AC:

1081

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

0.22

(source)

DANN

Benign

0.70

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over