rs12579350

Variant names:

• chr12-5687935-G-A
• rs12579350
• NM_001364791.2:c.1546-40134C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-5687935-G-A
• chr12-5687935-G-T

Variant summary

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

The NM_001364791.2(ANO2):​c.1546-40134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,178 control chromosomes in the GnomAD database, including 1,227 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 0.12 (1227 hom., cov: 33)
• Consequence: ANO2 NM_001364791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603
• Publications: 19 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364791.2. 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
	ANO2	NM_001364791.2	MANE Select	c.1546-40134C>T		intron	N/A	NP_001351720.1
	ANO2	NM_001278596.3		c.1561-40134C>T		intron	N/A	NP_001265525.1
	ANO2	NM_001278597.3		c.1549-40134C>T		intron	N/A	NP_001265526.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO2	ENST00000682330.1	MANE Select	c.1546-40134C>T		intron	N/A	ENSP00000507275.1
	ANO2	ENST00000650848.1		c.1561-40134C>T		intron	N/A	ENSP00000498903.1
	ANO2	ENST00000356134.9	TSL:5	c.1549-40134C>T		intron	N/A	ENSP00000348453.5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18145 AN: 152060 Hom.: 1224 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.119 AC: 18161 AN: 152178 Hom.: 1227 Cov.: 33 AF XY: 0.118 AC XY: 8748 AN XY: 74402

African (AFR) AF: 0.186 AC: 7703 AN: 41500

American (AMR) AF: 0.122 AC: 1866 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5178

South Asian (SAS) AF: 0.0859 AC: 415 AN: 4830

European-Finnish (FIN) AF: 0.0902 AC: 956 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5816 AN: 68002

Other (OTH) AF: 0.121 AC: 255 AN: 2114

Alfa AF: 0.0938 Hom.: 2291

Bravo AF: 0.123

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.70
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12579350; hg19: chr12-5797101;