chr12-5686285-T-A

Variant names:

• chr12-5686285-T-A
• rs387896
• NM_001364791.2:c.1546-38484A>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.1546-38484A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,184 control chromosomes in the GnomAD database, including 59,391 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 0.88 (59391 hom., cov: 32)
• Consequence: ANO2 NM_001364791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANO2	NM_001364791.2	c.1546-38484A>T		intron_variant	Intron 14 of 24	ENST00000682330.1	NP_001351720.1
ANO2	NM_001278596.3	c.1561-38484A>T		intron_variant	Intron 16 of 26		NP_001265525.1
ANO2	NM_001278597.3	c.1549-38484A>T		intron_variant	Intron 16 of 26		NP_001265526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO2	ENST00000682330.1	c.1546-38484A>T		intron_variant	Intron 14 of 24		NM_001364791.2	ENSP00000507275.1

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134257 AN: 152066 Hom.: 59362 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.883 AC: 134339 AN: 152184 Hom.: 59391 Cov.: 32 AF XY: 0.883 AC XY: 65727 AN XY: 74410

African (AFR) AF: 0.836 AC: 34696 AN: 41484

American (AMR) AF: 0.915 AC: 13999 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2956 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4918 AN: 5162

South Asian (SAS) AF: 0.868 AC: 4192 AN: 4828

European-Finnish (FIN) AF: 0.922 AC: 9783 AN: 10608

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60943 AN: 68010

Other (OTH) AF: 0.874 AC: 1848 AN: 2114

Alfa AF: 0.883 Hom.: 6935

Bravo AF: 0.882

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.35
PhyloP100		0.28
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: rs387896; hg19: chr12-5795451;