dbSNP rs56368827: KIF21B:c.*1226G>T (chr1-200972295-C-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.*1226G>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 0.255 in 152,110 control chromosomes in the GnomAD database, including 5,836 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 0.25 ( 5833 hom., cov: 32)

Exomes 𝑓: 0.19 ( 3 hom. )

Consequence

KIF21B
NM_001252102.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

7 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:

Genome browser will be placed here

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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
KIF21B	NM_001252102.2 link	c.*1226G>T	3_prime_UTR_variant	Exon 35 of 35	ENST00000461742.7	NP_001239031.1
KIF21B	NM_001252100.2 link	c.*1800G>T	3_prime_UTR_variant	Exon 35 of 35		NP_001239029.1
KIF21B	NM_017596.4 link	c.*1800G>T	3_prime_UTR_variant	Exon 34 of 34		NP_060066.2
KIF21B	NM_001252103.2 link	c.*1226G>T	3_prime_UTR_variant	Exon 34 of 34		NP_001239032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF21B	ENST00000461742.7 link	c.*1226G>T		3_prime_UTR_variant	Exon 35 of 35	1	NM_001252102.2	ENSP00000433808.1
KIF21B	ENST00000332129.6 link	c.*1800G>T		3_prime_UTR_variant	Exon 34 of 34	1		ENSP00000328494.2

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38680

AN:

151802

Hom.:

5835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.231

GnomAD4 exome

AF:

0.191

AC:

AN:

188

Hom.:

Cov.:

AF XY:

0.203

AC XY:

AN XY:

118

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.201

AC:

AN:

134

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.159

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

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:

0.255

AC:

38693

AN:

151922

Hom.:

5833

Cov.:

AF XY:

0.253

AC XY:

18811

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.416

AC:

17230

AN:

41442

American (AMR)

AF:

0.203

AC:

3109

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

609

AN:

3472

East Asian (EAS)

AF:

0.300

AC:

1543

AN:

5144

South Asian (SAS)

AF:

0.115

AC:

552

AN:

4814

European-Finnish (FIN)

AF:

0.247

AC:

2607

AN:

10556

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.182

AC:

12370

AN:

67894

Other (OTH)

AF:

0.230

AC:

484

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1371

2742

4113

5484

6855

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.218

Hom.:

860

Bravo

AF:

0.259

Asia WGS

AF:

0.218

AC:

756

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

0.16

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over