NM_018685.5:c.19-130C>G

Variant names:

• chr7-36396136-C-G
• rs10215150
• NM_018685.5:c.19-130C>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_018685.5(ANLN):​c.19-130C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 639,314 control chromosomes in the GnomAD database, including 11,681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.18 (2819 hom., cov: 32)
  • Exomes 𝑓: 0.18 (8862 hom.)
• Consequence: ANLN NM_018685.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.252

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 7-36396136-C-G is Benign according to our data. Variant chr7-36396136-C-G is described in ClinVar as [Benign]. Clinvar id is 1221148.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANLN	NM_018685.5	c.19-130C>G		intron_variant	Intron 1 of 23	ENST00000265748.7	NP_061155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANLN	ENST00000265748.7	c.19-130C>G		intron_variant	Intron 1 of 23	1	NM_018685.5	ENSP00000265748.2
ANLN	ENST00000396068.6	c.19-130C>G		intron_variant	Intron 1 of 22	1		ENSP00000379380.2
ANLN	ENST00000424865.1	c.-48-130C>G		intron_variant	Intron 1 of 3	3		ENSP00000404979.1
ANLN	ENST00000418118.1	c.-48-130C>G		intron_variant	Intron 1 of 1	3		ENSP00000406584.1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28082 AN: 151980 Hom.: 2816 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.182 AC: 88475 AN: 487218 Hom.: 8862 AF XY: 0.181 AC XY: 44186 AN XY: 243802

Gnomad4 AFR exome AF: 0.187

Gnomad4 AMR exome AF: 0.222

Gnomad4 ASJ exome AF: 0.201

Gnomad4 EAS exome AF: 0.392

Gnomad4 SAS exome AF: 0.265

Gnomad4 FIN exome AF: 0.186

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.185 AC: 28103 AN: 152096 Hom.: 2819 Cov.: 32 AF XY: 0.191 AC XY: 14186 AN XY: 74342

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.167

Alfa AF: 0.0728 Hom.: 87

Bravo AF: 0.186

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs10215150; hg19: chr7-36435745;