Variant chr7-36406246-A-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018685.5(ANLN):c.553A>C(p.Arg185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0896 in 1,613,920 control chromosomes in the GnomAD database, including 7,200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.077 ( 530 hom., cov: 33)

Exomes 𝑓: 0.091 ( 6670 hom. )

Consequence

ANLN
NM_018685.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.06

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 7-36406246-A-C is Benign according to our data. Variant chr7-36406246-A-C is described in ClinVar as [Benign]. Clinvar id is 261050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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.553A>C	p.Arg185=	synonymous_variant	4/24	ENST00000265748.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANLN	ENST00000265748.7 linkuse as main transcript	c.553A>C	p.Arg185=	synonymous_variant	4/24	1	NM_018685.5	P2	Q9NQW6-1
ANLN	ENST00000396068.6 linkuse as main transcript	c.553A>C	p.Arg185=	synonymous_variant	4/23	1		A2	Q9NQW6-2
ANLN	ENST00000424865.1 linkuse as main transcript	c.487A>C	p.Arg163=	synonymous_variant	4/4	3
ANLN	ENST00000460598.1 linkuse as main transcript	n.140A>C		non_coding_transcript_exon_variant	2/3	4

Frequencies

GnomAD3 genomes

AF:

0.0773

AC:

11769

AN:

152168

Hom.:

530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0511

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.0691

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.000960

Gnomad SAS

AF:

0.0252

Gnomad FIN

AF:

0.0576

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.0853

GnomAD3 exomes

AF:

0.0722

AC:

18145

AN:

251392

Hom.:

836

AF XY:

0.0720

AC XY:

9789

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.0495

Gnomad AMR exome

AF:

0.0490

Gnomad ASJ exome

AF:

0.0971

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0307

Gnomad FIN exome

AF:

0.0601

Gnomad NFE exome

AF:

0.105

Gnomad OTH exome

AF:

0.0830

GnomAD4 exome

AF:

0.0908

AC:

132776

AN:

1461634

Hom.:

6670

Cov.:

AF XY:

0.0895

AC XY:

65084

AN XY:

727070

show subpopulations

Gnomad4 AFR exome

AF:

0.0467

Gnomad4 AMR exome

AF:

0.0506

Gnomad4 ASJ exome

AF:

0.0937

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0293

Gnomad4 FIN exome

AF:

0.0658

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.0853

GnomAD4 genome

AF:

0.0774

AC:

11781

AN:

152286

Hom.:

530

Cov.:

AF XY:

0.0737

AC XY:

5485

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0514

Gnomad4 AMR

AF:

0.0689

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.000963

Gnomad4 SAS

AF:

0.0248

Gnomad4 FIN

AF:

0.0576

Gnomad4 NFE

AF:

0.105

Gnomad4 OTH

AF:

0.0840

Alfa

AF:

0.0957

Hom.:

381

Bravo

AF:

0.0768

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.103

EpiControl

AF:

0.104

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	Nov 29, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Mar 18, 2021	- -

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

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.5

DANN

Benign

0.66

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