2-241190072-G-A

Variant names:

• chr2-241190072-G-A
• rs11695874
• NM_001370694.2:c.9G>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001370694.2(ANO7):​c.9G>A​(p.Arg3Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,422,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R3R) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ANO7 NM_001370694.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 0 publications found

Genes affected

ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=0.145 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370694.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO7	NM_001370694.2	MANE Select	c.9G>A	p.Arg3Arg	synonymous	Exon 2 of 25	NP_001357623.1	A0A6I8PRE6
	ANO7	NM_001001666.4		c.9G>A	p.Arg3Arg	synonymous	Exon 2 of 4	NP_001001666.2	A0A6Q8JT31

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO7	ENST00000674324.2	MANE Select	c.9G>A	p.Arg3Arg	synonymous	Exon 2 of 25	ENSP00000501393.1	A0A6I8PRE6
	ANO7	ENST00000274979.12	TSL:1	c.171G>A	p.Arg57Arg	synonymous	Exon 2 of 25	ENSP00000274979.8	Q6IWH7-1
	ANO7	ENST00000402530.8	TSL:1	c.9G>A	p.Arg3Arg	synonymous	Exon 2 of 4	ENSP00000383985.4	A0A6Q8JT31

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000141 AC: 2 AN: 1422772 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 703998

African (AFR) AF: 0.00 AC: 0 AN: 32812

American (AMR) AF: 0.00 AC: 0 AN: 38770

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25388

East Asian (EAS) AF: 0.00 AC: 0 AN: 37722

South Asian (SAS) AF: 0.0000124 AC: 1 AN: 80908

European-Finnish (FIN) AF: 0.0000200 AC: 1 AN: 50114

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5608

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1092496

Other (OTH) AF: 0.00 AC: 0 AN: 58954

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.64
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs11695874; hg19: chr2-242129487;