Variant rs3815484 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018685.5(ANLN):c.2883+18C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,512,408 control chromosomes in the GnomAD database, including 11,895 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 941 hom., cov: 31)

Exomes 𝑓: 0.12 ( 10954 hom. )

Consequence

ANLN
NM_018685.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.503

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 7-36427046-C-A is Benign according to our data. Variant chr7-36427046-C-A is described in ClinVar as [Benign]. Clinvar id is 261049.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANLN	NM_018685.5 linkuse as main transcript	c.2883+18C>A		intron_variant		ENST00000265748.7	NP_061155.2	Q9NQW6-1A0A024RA49

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ANLN	ENST00000265748.7 linkuse as main transcript	c.2883+18C>A	intron_variant	1	NM_018685.5	ENSP00000265748.2	Q9NQW6-1
ANLN	ENST00000396068.6 linkuse as main transcript	c.2772+18C>A	intron_variant	1		ENSP00000379380.2	Q9NQW6-2
ANLN	ENST00000457743.1 linkuse as main transcript	c.492+18C>A	intron_variant	5		ENSP00000399553.1	H7C1C2
ANLN	ENST00000428612.5 linkuse as main transcript	c.375+18C>A	intron_variant	5		ENSP00000413522.1	H7C3S1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15501

AN:

151772

Hom.:

944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0510

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.0798

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.125

AC:

27850

AN:

222756

Hom.:

1949

AF XY:

0.128

AC XY:

15427

AN XY:

120588

show subpopulations

Gnomad AFR exome

AF:

0.0504

Gnomad AMR exome

AF:

0.0778

Gnomad ASJ exome

AF:

0.105

Gnomad EAS exome

AF:

0.224

Gnomad SAS exome

AF:

0.176

Gnomad FIN exome

AF:

0.139

Gnomad NFE exome

AF:

0.120

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.121

AC:

164719

AN:

1360522

Hom.:

10954

Cov.:

AF XY:

0.122

AC XY:

83294

AN XY:

680110

show subpopulations

Gnomad4 AFR exome

AF:

0.0470

Gnomad4 AMR exome

AF:

0.0742

Gnomad4 ASJ exome

AF:

0.0993

Gnomad4 EAS exome

AF:

0.243

Gnomad4 SAS exome

AF:

0.166

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.102

AC:

15510

AN:

151886

Hom.:

941

Cov.:

AF XY:

0.105

AC XY:

7763

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.0512

Gnomad4 AMR

AF:

0.0798

Gnomad4 ASJ

AF:

0.110

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.163

Gnomad4 FIN

AF:

0.135

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.0987

Alfa

AF:

0.115

Hom.:

1913

Bravo

AF:

0.0947

Asia WGS

AF:

0.181

AC:

628

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.2

DANN

Benign

0.48

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