10-27061127-G-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014915.3(ANKRD26):c.1462+17C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 1,527,490 control chromosomes in the GnomAD database, including 3,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.081 ( 579 hom., cov: 32)

Exomes 𝑓: 0.062 ( 2852 hom. )

Consequence

ANKRD26
NM_014915.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.0290

Publications

3 publications found

Variant links:

Genes affected

ANKRD26 (HGNC:29186): (ankyrin repeat domain containing 26) This gene encodes a protein containing N-terminal ankyrin repeats which function in protein-protein interactions. Mutations in this gene are associated with autosomal dominant thrombocytopenia-2. Pseudogenes of this gene are found on chromosome 7, 10, 13 and 16. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ANKRD26 Gene-Disease associations (from GenCC):

thrombocytopenia 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
acute myeloid leukemia
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
autosomal thrombocytopenia with normal platelets
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ANKRD26 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

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

BP6

Variant 10-27061127-G-T is Benign according to our data. Variant chr10-27061127-G-T is described in ClinVar as Benign. ClinVar VariationId is 260458.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014915.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD26	NM_014915.3	MANE Select	c.1462+17C>A		intron	N/A	NP_055730.2
	ANKRD26	NM_001256053.2		c.1462+17C>A		intron	N/A	NP_001242982.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ANKRD26	ENST00000376087.5	TSL:5 MANE Select	c.1462+17C>A	intron	N/A	ENSP00000365255.4
ANKRD26	ENST00000436985.7	TSL:1	c.1462+17C>A	intron	N/A	ENSP00000405112.3
ANKRD26	ENST00000674697.1		c.1111+17C>A	intron	N/A	ENSP00000502724.1

Frequencies

GnomAD3 genomes

AF:

0.0805

AC:

12238

AN:

151932

Hom.:

577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0436

Gnomad ASJ

AF:

0.0769

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.0842

Gnomad FIN

AF:

0.0640

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0569

Gnomad OTH

AF:

0.0823

GnomAD2 exomes

AF:

0.0688

AC:

17135

AN:

249000

AF XY:

0.0688

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.0394

Gnomad ASJ exome

AF:

0.0794

Gnomad EAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.0660

Gnomad NFE exome

AF:

0.0568

Gnomad OTH exome

AF:

0.0617

GnomAD4 exome

AF:

0.0616

AC:

84777

AN:

1375440

Hom.:

2852

Cov.:

AF XY:

0.0626

AC XY:

43150

AN XY:

689174

show subpopulations

African (AFR)

AF:

0.129

AC:

4071

AN:

31586

American (AMR)

AF:

0.0401

AC:

1787

AN:

44572

Ashkenazi Jewish (ASJ)

AF:

0.0792

AC:

2027

AN:

25582

East Asian (EAS)

AF:

0.103

AC:

4025

AN:

39170

South Asian (SAS)

AF:

0.0880

AC:

7431

AN:

84452

European-Finnish (FIN)

AF:

0.0710

AC:

3748

AN:

52824

Middle Eastern (MID)

AF:

0.0810

AC:

452

AN:

5582

European-Non Finnish (NFE)

AF:

0.0554

AC:

57298

AN:

1034132

Other (OTH)

AF:

0.0684

AC:

3938

AN:

57540

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

3588

7175

10763

14350

17938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2164

4328

6492

8656

10820

<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:

0.0806

AC:

12260

AN:

152050

Hom.:

579

Cov.:

AF XY:

0.0795

AC XY:

5905

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.132

AC:

5475

AN:

41466

American (AMR)

AF:

0.0435

AC:

664

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0769

AC:

267

AN:

3470

East Asian (EAS)

AF:

0.118

AC:

609

AN:

5168

South Asian (SAS)

AF:

0.0838

AC:

404

AN:

4820

European-Finnish (FIN)

AF:

0.0640

AC:

676

AN:

10558

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0569

AC:

3866

AN:

67982

Other (OTH)

AF:

0.0819

AC:

173

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

568

1136

1705

2273

2841

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

146

292

438

584

730

<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:

0.0441

Hom.:

Bravo

AF:

0.0813

Asia WGS

AF:

0.0920

AC:

320

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Nov 08, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Thrombocytopenia 2

Benign:2

Oct 30, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Dec 05, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.4

(source)

DANN

Benign

0.62

PhyloP100

-0.029

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over