Variant rs17213431 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.1857G>A(p.Val619=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,612,792 control chromosomes in the GnomAD database, including 14,460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.097 ( 923 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13537 hom. )

Consequence

ANLN
NM_018685.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.02

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=-0.58).

BP6

Variant 7-36419467-G-A is Benign according to our data. Variant chr7-36419467-G-A is described in ClinVar as [Benign]. Clinvar id is 1165187.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.02 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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.1857G>A	p.Val619=	synonymous_variant	10/24	ENST00000265748.7	NP_061155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANLN	ENST00000265748.7 linkuse as main transcript	c.1857G>A	p.Val619=	synonymous_variant	10/24	1	NM_018685.5	ENSP00000265748	P2	Q9NQW6-1
ANLN	ENST00000396068.6 linkuse as main transcript	c.1746G>A	p.Val582=	synonymous_variant	9/23	1		ENSP00000379380	A2	Q9NQW6-2
ANLN	ENST00000428612.5 linkuse as main transcript	c.97-5078G>A		intron_variant		5		ENSP00000413522

Frequencies

GnomAD3 genomes

AF:

0.0972

AC:

14782

AN:

152072

Hom.:

927

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.0723

Gnomad ASJ

AF:

0.0916

Gnomad EAS

AF:

0.0453

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.0879

GnomAD3 exomes

AF:

0.112

AC:

27937

AN:

250110

Hom.:

1851

AF XY:

0.118

AC XY:

16001

AN XY:

135214

show subpopulations

Gnomad AFR exome

AF:

0.0237

Gnomad AMR exome

AF:

0.0549

Gnomad ASJ exome

AF:

0.0928

Gnomad EAS exome

AF:

0.0347

Gnomad SAS exome

AF:

0.149

Gnomad FIN exome

AF:

0.171

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.132

AC:

192204

AN:

1460602

Hom.:

13537

Cov.:

AF XY:

0.133

AC XY:

96336

AN XY:

726654

show subpopulations

Gnomad4 AFR exome

AF:

0.0202

Gnomad4 AMR exome

AF:

0.0589

Gnomad4 ASJ exome

AF:

0.0925

Gnomad4 EAS exome

AF:

0.0563

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.161

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.0971

AC:

14776

AN:

152190

Hom.:

923

Cov.:

AF XY:

0.0978

AC XY:

7275

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0261

Gnomad4 AMR

AF:

0.0722

Gnomad4 ASJ

AF:

0.0916

Gnomad4 EAS

AF:

0.0456

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.0870

Alfa

AF:

0.121

Hom.:

2034

Bravo

AF:

0.0866

Asia WGS

AF:

0.0740

AC:

255

AN:

3478

EpiCase

AF:

0.134

EpiControl

AF:

0.137

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

8.1

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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