NM_018685.5:c.1857G>A

Variant names:

• chr7-36419467-G-A
• rs17213431
• NM_018685.5:c.1857G>A

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_018685.5(ANLN):​c.1857G>A​(p.Val619Val) 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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.02
• Publications: 20 publications found

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 Gene-Disease associations (from GenCC):

• focal segmental glomerulosclerosis 8

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• familial idiopathic steroid-resistant nephrotic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018685.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANLN	NM_018685.5	MANE Select	c.1857G>A	p.Val619Val	synonymous	Exon 10 of 24	NP_061155.2
	ANLN	NM_001284301.3		c.1746G>A	p.Val582Val	synonymous	Exon 9 of 23	NP_001271230.1
	ANLN	NM_001284302.3		c.1743G>A	p.Val581Val	synonymous	Exon 9 of 23	NP_001271231.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANLN	ENST00000265748.7	TSL:1 MANE Select	c.1857G>A	p.Val619Val	synonymous	Exon 10 of 24	ENSP00000265748.2
	ANLN	ENST00000396068.6	TSL:1	c.1746G>A	p.Val582Val	synonymous	Exon 9 of 23	ENSP00000379380.2
	ANLN	ENST00000428612.5	TSL:5	c.96-5078G>A		intron	N/A	ENSP00000413522.1

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14782 AN: 152072 Hom.: 927 Cov.: 32

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

GnomAD2 exomes AF: 0.112 AC: 27937 AN: 250110 AF XY: 0.118

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 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.: 32 AF XY: 0.133 AC XY: 96336 AN XY: 726654

African (AFR) AF: 0.0202 AC: 676 AN: 33470

American (AMR) AF: 0.0589 AC: 2634 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 2416 AN: 26132

East Asian (EAS) AF: 0.0563 AC: 2235 AN: 39682

South Asian (SAS) AF: 0.148 AC: 12789 AN: 86240

European-Finnish (FIN) AF: 0.161 AC: 8488 AN: 52718

Middle Eastern (MID) AF: 0.142 AC: 820 AN: 5766

European-Non Finnish (NFE) AF: 0.139 AC: 155002 AN: 1111508

Other (OTH) AF: 0.118 AC: 7144 AN: 60372

GnomAD4 genome AF: 0.0971 AC: 14776 AN: 152190 Hom.: 923 Cov.: 32 AF XY: 0.0978 AC XY: 7275 AN XY: 74388

African (AFR) AF: 0.0261 AC: 1085 AN: 41552

American (AMR) AF: 0.0722 AC: 1105 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3470

East Asian (EAS) AF: 0.0456 AC: 236 AN: 5178

South Asian (SAS) AF: 0.141 AC: 677 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1846 AN: 10550

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9161 AN: 68006

Other (OTH) AF: 0.0870 AC: 184 AN: 2116

Alfa AF: 0.119 Hom.: 2395

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

Submissions by phenotype

not provided Benign:2

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.1
DANN	Benign	0.75
PhyloP100		1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17213431; hg19: chr7-36459076; COSMIC: COSV56078284; COSMIC: COSV56078284;