chr7-36450989-G-T

Position:

• chr7-36450989-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018685.5(ANLN):​c.3251+1152G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,080 control chromosomes in the GnomAD database, including 18,876 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (18876 hom., cov: 32)
• Consequence: ANLN NM_018685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANLN	NM_018685.5	c.3251+1152G>T		intron_variant		ENST00000265748.7	NP_061155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANLN	ENST00000265748.7	c.3251+1152G>T		intron_variant		1	NM_018685.5	ENSP00000265748	P2
ANLN	ENST00000396068.6	c.3140+1152G>T		intron_variant		1		ENSP00000379380	A2
ANLN	ENST00000491782.1	n.899+1152G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75300 AN: 151962 Hom.: 18847 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.496 AC: 75390 AN: 152080 Hom.: 18876 Cov.: 32 AF XY: 0.499 AC XY: 37118 AN XY: 74328

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.486

Alfa AF: 0.504 Hom.: 3324

Bravo AF: 0.493

Asia WGS AF: 0.604 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.69

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: rs3801303; hg19: chr7-36490598;