rs2304871

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000037.4(ANK1):c.315C>T(p.Asn105Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,613,572 control chromosomes in the GnomAD database, including 58,122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 4494 hom., cov: 32)

Exomes 𝑓: 0.27 ( 53628 hom. )

Consequence

ANK1
NM_000037.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -0.714

Variant links:

Genes affected

ANK1 (HGNC:492): (ankyrin 1) Ankyrins are a family of proteins that link the integral membrane proteins to the underlying spectrin-actin cytoskeleton and play key roles in activities such as cell motility, activation, proliferation, contact and the maintenance of specialized membrane domains. Multiple isoforms of ankyrin with different affinities for various target proteins are expressed in a tissue-specific, developmentally regulated manner. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. Ankyrin 1, the prototype of this family, was first discovered in the erythrocytes, but since has also been found in brain and muscles. Mutations in erythrocytic ankyrin 1 have been associated in approximately half of all patients with hereditary spherocytosis. Complex patterns of alternative splicing in the regulatory domain, giving rise to different isoforms of ankyrin 1 have been described. Truncated muscle-specific isoforms of ankyrin 1 resulting from usage of an alternate promoter have also been identified. [provided by RefSeq, Dec 2008]

ANK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 8-41727920-G-A is Benign according to our data. Variant chr8-41727920-G-A is described in ClinVar as [Benign]. Clinvar id is 261304.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-41727920-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.714 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANK1	NM_000037.4 link	c.315C>T	p.Asn105Asn	synonymous_variant	Exon 4 of 43	ENST00000289734.13	NP_000028.3	P16157-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANK1	ENST00000289734.13 link	c.315C>T	p.Asn105Asn	synonymous_variant	Exon 4 of 43	1	NM_000037.4	ENSP00000289734.8		P16157-3

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36345

AN:

152010

Hom.:

4488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.241

AC:

60622

AN:

251384

Hom.:

7842

AF XY:

0.249

AC XY:

33812

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.187

Gnomad AMR exome

AF:

0.138

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.193

Gnomad SAS exome

AF:

0.256

Gnomad FIN exome

AF:

0.213

Gnomad NFE exome

AF:

0.279

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.268

AC:

391016

AN:

1461444

Hom.:

53628

Cov.:

AF XY:

0.269

AC XY:

195343

AN XY:

727058

show subpopulations

Gnomad4 AFR exome

AF:

0.184

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.344

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.256

Gnomad4 FIN exome

AF:

0.217

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.239

AC:

36357

AN:

152128

Hom.:

4494

Cov.:

AF XY:

0.236

AC XY:

17531

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.340

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.260

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.261

Hom.:

4111

Bravo

AF:

0.238

Asia WGS

AF:

0.232

AC:

806

AN:

3478

EpiCase

AF:

0.292

EpiControl

AF:

0.296

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary spherocytosis type 1

Benign:5

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 22, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Jul 28, 2017

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

- -

Spherocytosis

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

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

-0.80

CADD

Benign

1.7

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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

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