Variant rs61549495 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBA1

The NM_018685.5(ANLN):c.883_885dup(p.Ser295dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,606,298 control chromosomes in the GnomAD database, including 131,825 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11794 hom., cov: 0)

Exomes 𝑓: 0.40 ( 120031 hom. )

Consequence

ANLN
NM_018685.5 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.593

Variant links:

Genes affected

ANLN (HGNC:14082): (anillin, actin binding protein) This gene encodes an actin-binding protein that plays a role in cell growth and migration, and in cytokinesis. The encoded protein is thought to regulate actin cytoskeletal dynamics in podocytes, components of the glomerulus. Mutations in this gene are associated with focal segmental glomerulosclerosis 8. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]

ANLN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_018685.5. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 7-36407740-A-ACTT is Benign according to our data. Variant chr7-36407740-A-ACTT is described in ClinVar as [Benign]. Clinvar id is 261052.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANLN	NM_018685.5 linkuse as main transcript	c.883_885dup	p.Ser295dup	inframe_insertion	5/24	ENST00000265748.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANLN	ENST00000265748.7 linkuse as main transcript	c.883_885dup	p.Ser295dup	inframe_insertion	5/24	1	NM_018685.5	P2	Q9NQW6-1

Frequencies

GnomAD3 genomes

AF:

0.390

AC:

59157

AN:

151578

Hom.:

11780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.477

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.469

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.371

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.405

GnomAD3 exomes

AF:

0.434

AC:

108843

AN:

250590

Hom.:

24509

AF XY:

0.430

AC XY:

58310

AN XY:

135508

show subpopulations

Gnomad AFR exome

AF:

0.339

Gnomad AMR exome

AF:

0.553

Gnomad ASJ exome

AF:

0.469

Gnomad EAS exome

AF:

0.600

Gnomad SAS exome

AF:

0.453

Gnomad FIN exome

AF:

0.377

Gnomad NFE exome

AF:

0.388

Gnomad OTH exome

AF:

0.434

GnomAD4 exome

AF:

0.402

AC:

585388

AN:

1454602

Hom.:

120031

Cov.:

AF XY:

0.404

AC XY:

292228

AN XY:

724078

show subpopulations

Gnomad4 AFR exome

AF:

0.334

Gnomad4 AMR exome

AF:

0.538

Gnomad4 ASJ exome

AF:

0.468

Gnomad4 EAS exome

AF:

0.587

Gnomad4 SAS exome

AF:

0.445

Gnomad4 FIN exome

AF:

0.378

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.412

GnomAD4 genome

AF:

0.390

AC:

59224

AN:

151696

Hom.:

11794

Cov.:

AF XY:

0.393

AC XY:

29103

AN XY:

74140

show subpopulations

Gnomad4 AFR

AF:

0.335

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.469

Gnomad4 EAS

AF:

0.584

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.371

Gnomad4 NFE

AF:

0.390

Gnomad4 OTH

AF:

0.406

Alfa

AF:

0.405

Hom.:

8043

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Focal segmental glomerulosclerosis 8

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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