2-241190416-A-G

Variant names:

• chr2-241190416-A-G
• rs4675826
• NM_001370694.2:c.108+245A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001370694.2(ANO7):​c.108+245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,218 control chromosomes in the GnomAD database, including 2,442 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (2442 hom., cov: 33)
• Consequence: ANO7 NM_001370694.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.17
• 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: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 2-241190416-A-G is Benign according to our data. Variant chr2-241190416-A-G is described in ClinVar as Benign. ClinVar VariationId is 1260208.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

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.108+245A>G		intron	N/A	NP_001357623.1	A0A6I8PRE6
	ANO7	NM_001001666.4		c.108+245A>G		intron	N/A	NP_001001666.2	A0A6Q8JT31

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO7	ENST00000674324.2	MANE Select	c.108+245A>G		intron	N/A	ENSP00000501393.1	A0A6I8PRE6
	ANO7	ENST00000274979.12	TSL:1	c.270+245A>G		intron	N/A	ENSP00000274979.8	Q6IWH7-1
	ANO7	ENST00000402530.8	TSL:1	c.108+245A>G		intron	N/A	ENSP00000383985.4	A0A6Q8JT31

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20387 AN: 152100 Hom.: 2427 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.0237

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.134 AC: 20429 AN: 152218 Hom.: 2442 Cov.: 33 AF XY: 0.143 AC XY: 10655 AN XY: 74422

African (AFR) AF: 0.146 AC: 6083 AN: 41552

American (AMR) AF: 0.261 AC: 3990 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0237 AC: 82 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3207 AN: 5152

South Asian (SAS) AF: 0.122 AC: 590 AN: 4828

European-Finnish (FIN) AF: 0.143 AC: 1516 AN: 10600

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4621 AN: 67992

Other (OTH) AF: 0.141 AC: 298 AN: 2114

Alfa AF: 0.0924 Hom.: 154

Bravo AF: 0.150

Asia WGS AF: 0.334 AC: 1157 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.46
PhyloP100		-1.2
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: rs4675826; hg19: chr2-242129831;