chr12-5551171-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO2	ENST00000536751.1	n.92+12075A>G		intron_variant	Intron 1 of 2	3

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

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.503

Alfa AF: 0.538 Hom.: 21755

Bravo AF: 0.510

Asia WGS AF: 0.727 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12582976; hg19: chr12-5660337;