NM_001364791.2:c.2234-5501A>T

Variant names:

• chr12-5584019-T-A
• rs11537531
• NM_001364791.2:c.2234-5501A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001364791.2(ANO2):​c.2234-5501A>T variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ANO2 NM_001364791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.73
• Publications: 0 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]

ENSG00000255973 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANO2	NM_001364791.2	c.2234-5501A>T		intron_variant	Intron 20 of 24	ENST00000682330.1	NP_001351720.1
LOC101901829		n.5584019T>A		intragenic_variant
ANO2	NM_001278596.3	c.2249-5501A>T		intron_variant	Intron 22 of 26		NP_001265525.1
ANO2	NM_001278597.3	c.2237-5501A>T		intron_variant	Intron 22 of 26		NP_001265526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO2	ENST00000682330.1	c.2234-5501A>T		intron_variant	Intron 20 of 24		NM_001364791.2	ENSP00000507275.1
ENSG00000255973	ENST00000545761.1	n.223T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ANO2	ENST00000650848.1	c.2249-5501A>T		intron_variant	Intron 22 of 26			ENSP00000498903.1
ANO2	ENST00000356134.9	c.2237-5501A>T		intron_variant	Intron 22 of 26	5		ENSP00000348453.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.0
DANN	Benign	0.66
PhyloP100		4.7

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: rs11537531; hg19: chr12-5693185;