10-27038070-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_014915.3(ANKRD26):c.2376-16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 1,594,244 control chromosomes in the GnomAD database, including 538,203 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 53286 hom., cov: 31)

Exomes 𝑓: 0.82 ( 484917 hom. )

Consequence

ANKRD26
NM_014915.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.50

Publications

11 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 -16 ACMG points.

BP6

Variant 10-27038070-T-C is Benign according to our data. Variant chr10-27038070-T-C is described in ClinVar as [Benign]. Clinvar id is 260461.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD26	NM_014915.3 link	c.2376-16A>G		intron_variant	Intron 21 of 33	ENST00000376087.5	NP_055730.2	Q9UPS8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD26	ENST00000376087.5 link	c.2376-16A>G		intron_variant	Intron 21 of 33	5	NM_014915.3	ENSP00000365255.4		Q9UPS8-1

Frequencies

GnomAD3 genomes

AF:

0.835

AC:

126928

AN:

152012

Hom.:

53251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.799

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.837

Gnomad EAS

AF:

0.989

Gnomad SAS

AF:

0.891

Gnomad FIN

AF:

0.910

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.809

Gnomad OTH

AF:

0.818

GnomAD2 exomes

AF:

0.834

AC:

202160

AN:

242428

AF XY:

0.837

show subpopulations

Gnomad AFR exome

AF:

0.860

Gnomad AMR exome

AF:

0.731

Gnomad ASJ exome

AF:

0.832

Gnomad EAS exome

AF:

0.992

Gnomad FIN exome

AF:

0.910

Gnomad NFE exome

AF:

0.812

Gnomad OTH exome

AF:

0.822

GnomAD4 exome

AF:

0.819

AC:

1180739

AN:

1442114

Hom.:

484917

Cov.:

AF XY:

0.821

AC XY:

589628

AN XY:

718370

show subpopulations

African (AFR)

AF:

0.862

AC:

28550

AN:

33138

American (AMR)

AF:

0.731

AC:

32480

AN:

44430

Ashkenazi Jewish (ASJ)

AF:

0.833

AC:

21646

AN:

26000

East Asian (EAS)

AF:

0.985

AC:

38845

AN:

39444

South Asian (SAS)

AF:

0.877

AC:

75141

AN:

85714

European-Finnish (FIN)

AF:

0.903

AC:

42237

AN:

46798

Middle Eastern (MID)

AF:

0.801

AC:

4433

AN:

5536

European-Non Finnish (NFE)

AF:

0.806

AC:

887893

AN:

1101206

Other (OTH)

AF:

0.827

AC:

49514

AN:

59848

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

9584

19168

28751

38335

47919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.835

AC:

127015

AN:

152130

Hom.:

53286

Cov.:

AF XY:

0.843

AC XY:

62709

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.862

AC:

35781

AN:

41520

American (AMR)

AF:

0.760

AC:

11607

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.837

AC:

2901

AN:

3468

East Asian (EAS)

AF:

0.989

AC:

5104

AN:

5160

South Asian (SAS)

AF:

0.891

AC:

4300

AN:

4824

European-Finnish (FIN)

AF:

0.910

AC:

9620

AN:

10574

Middle Eastern (MID)

AF:

0.776

AC:

228

AN:

294

European-Non Finnish (NFE)

AF:

0.809

AC:

55013

AN:

67984

Other (OTH)

AF:

0.819

AC:

1734

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1061

2123

3184

4246

5307

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.815

Hom.:

16692

Bravo

AF:

0.823

Asia WGS

AF:

0.929

AC:

3214

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Aug 10, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

- -

Thrombocytopenia 2

Benign:2

Nov 27, 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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

(source)

DANN

Benign

0.51

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.29

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.29

Position offset: 12

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

10-27038070-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over