chr10-27004354-CA-C

Variant names:

• chr10-27004354-CA-C
• rs112091269
• NM_014915.3:c.*1235delT

Variant summary

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

The NM_014915.3(ANKRD26):​c.*1235delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 151,908 control chromosomes in the GnomAD database, including 786 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.094 (786 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ANKRD26 NM_014915.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.501

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 10-27004354-CA-C is Benign according to our data. Variant chr10-27004354-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 299710.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD26	NM_014915.3	c.*1235delT		3_prime_UTR_variant	Exon 34 of 34	ENST00000376087.5	NP_055730.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD26	ENST00000376087	c.*1235delT		3_prime_UTR_variant	Exon 34 of 34	5	NM_014915.3	ENSP00000365255.4

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14187 AN: 151792 Hom.: 772 Cov.: 31

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.101

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0937 AC: 14230 AN: 151908 Hom.: 786 Cov.: 31 AF XY: 0.0995 AC XY: 7386 AN XY: 74238

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0285 Hom.: 22

Bravo AF: 0.0899

Asia WGS AF: 0.242 AC: 838 AN: 3474

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Thrombocytopenia Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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: rs112091269; hg19: chr10-27293283;