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rs17213431

chr7-36419467-G-Achr7-36419467-G-T

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

2

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.02 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
ANLNNM_018685.5 linkuse as main transcriptc.1857G>A p.Val619= synonymous_variant 10/24 ENST00000265748.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANLNENST00000265748.7 linkuse as main transcriptc.1857G>A p.Val619= synonymous_variant 10/241 NM_018685.5 P2Q9NQW6-1
ANLNENST00000396068.6 linkuse as main transcriptc.1746G>A p.Val582= synonymous_variant 9/231 A2Q9NQW6-2
ANLNENST00000428612.5 linkuse as main transcriptc.97-5078G>A intron_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0972
AC:
14782
AN:
152072
Hom.:
927
Cov.:
32
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.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0971
AC:
14776
AN:
152190
Hom.:
923
Cov.:
32
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 submitterclinical testingGeneDxNov 10, 2018- -
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

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.

Other links and lift over

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