NM_000037.4:c.2913G>C

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.2913G>C(p.Leu971Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,613,058 control chromosomes in the GnomAD database, including 178,758 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 13836 hom., cov: 33)

Exomes 𝑓: 0.47 ( 164922 hom. )

Consequence

ANK1
NM_000037.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 2.13

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 8-41696410-C-G is Benign according to our data. Variant chr8-41696410-C-G is described in ClinVar as [Benign]. Clinvar id is 261301.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-41696410-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=2.13 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANK1	NM_000037.4 link	c.2913G>C	p.Leu971Leu	synonymous_variant	Exon 26 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.2913G>C	p.Leu971Leu	synonymous_variant	Exon 26 of 43	1	NM_000037.4	ENSP00000289734.8		P16157-3

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

60093

AN:

152022

Hom.:

13834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.506

Gnomad ASJ

AF:

0.436

Gnomad EAS

AF:

0.514

Gnomad SAS

AF:

0.510

Gnomad FIN

AF:

0.578

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.417

GnomAD3 exomes

AF:

0.485

AC:

120957

AN:

249342

Hom.:

30707

AF XY:

0.487

AC XY:

65883

AN XY:

135236

show subpopulations

Gnomad AFR exome

AF:

0.138

Gnomad AMR exome

AF:

0.603

Gnomad ASJ exome

AF:

0.440

Gnomad EAS exome

AF:

0.539

Gnomad SAS exome

AF:

0.509

Gnomad FIN exome

AF:

0.560

Gnomad NFE exome

AF:

0.473

Gnomad OTH exome

AF:

0.479

GnomAD4 exome

AF:

0.470

AC:

686948

AN:

1460918

Hom.:

164922

Cov.:

AF XY:

0.472

AC XY:

343014

AN XY:

726788

show subpopulations

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.590

Gnomad4 ASJ exome

AF:

0.428

Gnomad4 EAS exome

AF:

0.527

Gnomad4 SAS exome

AF:

0.505

Gnomad4 FIN exome

AF:

0.555

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.465

GnomAD4 genome

AF:

0.395

AC:

60100

AN:

152140

Hom.:

13836

Cov.:

AF XY:

0.406

AC XY:

30182

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.506

Gnomad4 ASJ

AF:

0.436

Gnomad4 EAS

AF:

0.514

Gnomad4 SAS

AF:

0.509

Gnomad4 FIN

AF:

0.578

Gnomad4 NFE

AF:

0.473

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.372

Hom.:

1985

Bravo

AF:

0.381

Asia WGS

AF:

0.506

AC:

1759

AN:

3478

EpiCase

AF:

0.469

EpiControl

AF:

0.467

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary spherocytosis type 1

Benign:5

Oct 10, 2014

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

- -

Nov 29, 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. -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

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

-0.50

CADD

Benign

6.6

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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