Genetic Variant NM_001252102.2:c.*933C>T (chr1-200972588-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.*933C>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 0.276 in 152,716 control chromosomes in the GnomAD database, including 6,583 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 ( 6560 hom., cov: 33)

Exomes 𝑓: 0.29 ( 23 hom. )

Consequence

KIF21B
NM_001252102.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.405

Publications

10 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=-0.69).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KIF21B	NM_001252102.2 link	c.*933C>T	3_prime_UTR_variant	Exon 35 of 35	ENST00000461742.7	NP_001239031.1	O75037-4
KIF21B	NM_001252100.2 link	c.*1507C>T	3_prime_UTR_variant	Exon 35 of 35		NP_001239029.1	O75037-1Q2UVF0
KIF21B	NM_017596.4 link	c.*1507C>T	3_prime_UTR_variant	Exon 34 of 34		NP_060066.2	O75037-2
KIF21B	NM_001252103.2 link	c.*933C>T	3_prime_UTR_variant	Exon 34 of 34		NP_001239032.1	O75037-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF21B	ENST00000461742.7 link	c.*933C>T		3_prime_UTR_variant	Exon 35 of 35	1	NM_001252102.2	ENSP00000433808.1		O75037-4
KIF21B	ENST00000332129.6 link	c.*1507C>T		3_prime_UTR_variant	Exon 34 of 34	1		ENSP00000328494.2		O75037-2

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

42017

AN:

152006

Hom.:

6549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.361

Gnomad EAS

AF:

0.238

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.314

GnomAD4 exome

AF:

0.285

AC:

169

AN:

592

Hom.:

Cov.:

AF XY:

0.276

AC XY:

102

AN XY:

370

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.300

AC:

126

AN:

420

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.261

AC:

AN:

142

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.529

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.276

AC:

42033

AN:

152124

Hom.:

6560

Cov.:

AF XY:

0.282

AC XY:

20995

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.134

AC:

5554

AN:

41550

American (AMR)

AF:

0.383

AC:

5858

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.361

AC:

1252

AN:

3470

East Asian (EAS)

AF:

0.239

AC:

1231

AN:

5152

South Asian (SAS)

AF:

0.459

AC:

2220

AN:

4832

European-Finnish (FIN)

AF:

0.324

AC:

3429

AN:

10590

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21574

AN:

67912

Other (OTH)

AF:

0.309

AC:

651

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1555

3110

4666

6221

7776

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<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:

0.210

Hom.:

587

Bravo

AF:

0.272

Asia WGS

AF:

0.310

AC:

1082

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.41

Mutation Taster

=98/2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over