Variant 10-27061127-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD26	NM_014915.3 linkuse as main transcript	c.1462+17C>A		intron_variant		ENST00000376087.5	NP_055730.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD26	ENST00000376087.5 linkuse as main transcript	c.1462+17C>A		intron_variant		5	NM_014915.3	ENSP00000365255	A2	Q9UPS8-1

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

GnomAD3 exomes

AF:

0.0688

AC:

17135

AN:

249000

Hom.:

683

AF XY:

0.0688

AC XY:

9302

AN XY:

135120

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 SAS exome

AF:

0.0866

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

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.0401

Gnomad4 ASJ exome

AF:

0.0792

Gnomad4 EAS exome

AF:

0.103

Gnomad4 SAS exome

AF:

0.0880

Gnomad4 FIN exome

AF:

0.0710

Gnomad4 NFE exome

AF:

0.0554

Gnomad4 OTH exome

AF:

0.0684

GnomAD4 genome

AF:

0.0806

AC:

12260

AN:

152050

Hom.:

579

Cov.:

AF XY:

0.0795

AC XY:

5905

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.132

Gnomad4 AMR

AF:

0.0435

Gnomad4 ASJ

AF:

0.0769

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.0838

Gnomad4 FIN

AF:

0.0640

Gnomad4 NFE

AF:

0.0569

Gnomad4 OTH

AF:

0.0819

Alfa

AF:

0.0417

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 08, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Thrombocytopenia 2

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 18, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.4

DANN

Benign

0.62

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over