12-5551171-T-C

Variant names:

• chr12-5551171-T-C
• rs12582976
• ENST00000536751.1:n.92+12075A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536751.1(ANO2):​n.92+12075A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,996 control chromosomes in the GnomAD database, including 21,335 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 0.52 (21335 hom., cov: 33)
• Consequence: ANO2 ENST00000536751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 1 publications found

Genes affected

ANO2 (HGNC:1183): (anoctamin 2) ANO2 belongs to a family of calcium-activated chloride channels (CaCCs) (reviewed by Hartzell et al., 2009 [PubMed 19015192]).[supplied by OMIM, Jan 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536751.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO2	ENST00000536751.1	TSL:3	n.92+12075A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78510 AN: 151876 Hom.: 21329 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.517 AC: 78554 AN: 151996 Hom.: 21335 Cov.: 33 AF XY: 0.523 AC XY: 38868 AN XY: 74278

African (AFR) AF: 0.367 AC: 15198 AN: 41448

American (AMR) AF: 0.582 AC: 8895 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1945 AN: 3466

East Asian (EAS) AF: 0.843 AC: 4351 AN: 5164

South Asian (SAS) AF: 0.653 AC: 3148 AN: 4822

European-Finnish (FIN) AF: 0.577 AC: 6077 AN: 10526

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37243 AN: 67960

Other (OTH) AF: 0.503 AC: 1061 AN: 2110

Alfa AF: 0.522 Hom.: 32335

Bravo AF: 0.510

Asia WGS AF: 0.727 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.75
PhyloP100		0.068

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12582976; hg19: chr12-5660337;