10-27004774-G-GA

Position:

• chr10-27004774-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_014915.3(ANKRD26):​c.*815dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,500 control chromosomes in the GnomAD database, including 1,151 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1150 hom., cov: 31)
  • Exomes 𝑓: 0.070 (1 hom.)
• Consequence: ANKRD26 NM_014915.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00600

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-27004774-G-GA is Benign according to our data. Variant chr10-27004774-G-GA is described in ClinVar as [Likely_benign]. Clinvar id is 299718.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD26	NM_014915.3	c.*815dupT		3_prime_UTR_variant	34/34	ENST00000376087.5	NP_055730.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD26	ENST00000376087	c.*815dupT		3_prime_UTR_variant	34/34	5	NM_014915.3	ENSP00000365255.4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16119 AN: 152026 Hom.: 1148 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0933

GnomAD4 exome AF: 0.0698 AC: 25 AN: 358 Hom.: 1 Cov.: 2 AF XY: 0.0688 AC XY: 11 AN XY: 160

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.167

Gnomad4 NFE exome AF: 0.0680

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.106 AC: 16141 AN: 152142 Hom.: 1150 Cov.: 31 AF XY: 0.110 AC XY: 8206 AN XY: 74358

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0861

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0864 Hom.: 76

Bravo AF: 0.103

Asia WGS AF: 0.215 AC: 745 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Thrombocytopenia Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs397845107; hg19: chr10-27293703;