Variant 10-27038070-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_014915.3(ANKRD26):c.2376-16A>G variant causes a splice polypyrimidine tract, 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 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.50

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 -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. Variant chr10-27038070-T-C is described in Lovd as [Benign].

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/exons	MANE	UniProt
ANKRD26	NM_014915.3 linkuse as main transcript	c.2376-16A>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000376087.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD26	ENST00000376087.5 linkuse as main transcript	c.2376-16A>G		splice_polypyrimidine_tract_variant, intron_variant		5	NM_014915.3	A2	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

GnomAD3 exomes

AF:

0.834

AC:

202160

AN:

242428

Hom.:

84778

AF XY:

0.837

AC XY:

110423

AN XY:

131944

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 SAS exome

AF:

0.881

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

Gnomad4 AFR exome

AF:

0.862

Gnomad4 AMR exome

AF:

0.731

Gnomad4 ASJ exome

AF:

0.833

Gnomad4 EAS exome

AF:

0.985

Gnomad4 SAS exome

AF:

0.877

Gnomad4 FIN exome

AF:

0.903

Gnomad4 NFE exome

AF:

0.806

Gnomad4 OTH exome

AF:

0.827

GnomAD4 genome

AF:

0.835

AC:

127015

AN:

152130

Hom.:

53286

Cov.:

AF XY:

0.843

AC XY:

62709

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.862

Gnomad4 AMR

AF:

0.760

Gnomad4 ASJ

AF:

0.837

Gnomad4 EAS

AF:

0.989

Gnomad4 SAS

AF:

0.891

Gnomad4 FIN

AF:

0.910

Gnomad4 NFE

AF:

0.809

Gnomad4 OTH

AF:

0.819

Alfa

AF:

0.817

Hom.:

9477

Bravo

AF:

0.823

Asia WGS

AF:

0.929

AC:

3214

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Thrombocytopenia 2

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 16, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Dec 05, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 10, 2019	- -

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

-0.97

CADD

Benign

DANN

Benign

0.51

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

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