chr12-5625021-A-G

Position:

• chr12-5625021-A-G

Variant summary

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

The NM_001364791.2(ANO2):​c.1817-9724T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,056 control chromosomes in the GnomAD database, including 7,368 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 0.29 (7368 hom., cov: 32)
• Consequence: ANO2 NM_001364791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

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]

ANO2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANO2	NM_001364791.2	c.1817-9724T>C		intron_variant		ENST00000682330.1	NP_001351720.1
ANO2	NM_001278596.3	c.1832-9724T>C		intron_variant			NP_001265525.1
ANO2	NM_001278597.3	c.1820-9724T>C		intron_variant			NP_001265526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO2	ENST00000682330.1	c.1817-9724T>C		intron_variant			NM_001364791.2	ENSP00000507275.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43363 AN: 151938 Hom.: 7374 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.285 AC: 43354 AN: 152056 Hom.: 7368 Cov.: 32 AF XY: 0.285 AC XY: 21194 AN XY: 74312

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.290

Alfa AF: 0.307 Hom.: 1270

Bravo AF: 0.271

Asia WGS AF: 0.402 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.63

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: rs2110169; hg19: chr12-5734187;