dbSNP rs1547350: KIF26A:c.*199A>C (chr14-104179989-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015656.2(KIF26A):c.*199A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 507,532 control chromosomes in the GnomAD database, including 74,202 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 0.53 ( 21839 hom., cov: 31)

Exomes 𝑓: 0.54 ( 52363 hom. )

Consequence

KIF26A
NM_015656.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435

Publications

9 publications found

Variant links:

Genes affected

KIF26A (HGNC:20226): (kinesin family member 26A) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in enteric nervous system development; negative regulation of signal transduction; and regulation of cell growth by extracellular stimulus. Predicted to be located in cytosol. Predicted to be part of kinesin complex. Predicted to be active in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

KIF26A Gene-Disease associations (from GenCC):

cortical dysplasia, complex, with other brain malformations 11
Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Baylor College of Medicine Research Center

KIF26A 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26A	NM_015656.2 link	c.*199A>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000423312.7	NP_056471.1	Q9ULI4
KIF26A	XM_011536641.3 link	c.*199A>C		3_prime_UTR_variant	Exon 12 of 12		XP_011534943.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIF26A	ENST00000423312.7 link	c.*199A>C	3_prime_UTR_variant	Exon 15 of 15	5	NM_015656.2	ENSP00000388241.2	Q9ULI4
KIF26A	ENST00000315264.7 link	c.*199A>C	3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000325452.7	C9JFF0
KIF26A	ENST00000697132.1 link	c.*199A>C	3_prime_UTR_variant	Exon 15 of 15			ENSP00000513129.1	A0A8V8TM02

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

80966

AN:

151720

Hom.:

21811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.505

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.644

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.522

Gnomad OTH

AF:

0.527

GnomAD4 exome

AF:

0.536

AC:

190557

AN:

355694

Hom.:

52363

Cov.:

AF XY:

0.534

AC XY:

97911

AN XY:

183230

show subpopulations

African (AFR)

AF:

0.496

AC:

4534

AN:

9146

American (AMR)

AF:

0.691

AC:

7602

AN:

11004

Ashkenazi Jewish (ASJ)

AF:

0.508

AC:

5631

AN:

11092

East Asian (EAS)

AF:

0.649

AC:

16076

AN:

24758

South Asian (SAS)

AF:

0.529

AC:

10505

AN:

19864

European-Finnish (FIN)

AF:

0.522

AC:

12896

AN:

24704

Middle Eastern (MID)

AF:

0.501

AC:

822

AN:

1642

European-Non Finnish (NFE)

AF:

0.521

AC:

120925

AN:

232156

Other (OTH)

AF:

0.542

AC:

11566

AN:

21328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

4452

8905

13357

17810

22262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1040

2080

3120

4160

5200

<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:

0.534

AC:

81042

AN:

151838

Hom.:

21839

Cov.:

AF XY:

0.537

AC XY:

39815

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.504

AC:

20868

AN:

41378

American (AMR)

AF:

0.655

AC:

10006

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.509

AC:

1766

AN:

3470

East Asian (EAS)

AF:

0.643

AC:

3303

AN:

5134

South Asian (SAS)

AF:

0.549

AC:

2645

AN:

4820

European-Finnish (FIN)

AF:

0.515

AC:

5445

AN:

10570

Middle Eastern (MID)

AF:

0.497

AC:

145

AN:

292

European-Non Finnish (NFE)

AF:

0.522

AC:

35440

AN:

67890

Other (OTH)

AF:

0.532

AC:

1121

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1977

3955

5932

7910

9887

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<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:

0.524

Hom.:

37250

Bravo

AF:

0.542

Asia WGS

AF:

0.595

AC:

2065

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.38

(source)

DANN

Benign

0.57

PhyloP100

-0.43

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