chr2-241190416-A-G

Position:

• chr2-241190416-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2	c.108+245A>G		intron_variant		ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000674324.2	c.108+245A>G		intron_variant			NM_001370694.2	A2
ANO7	ENST00000274979.12	c.270+245A>G		intron_variant		1		P2
ANO7	ENST00000402530.8	c.108+245A>G		intron_variant		1
ANO7	ENST00000402430.8	c.108+245A>G		intron_variant		5

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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.0237

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0924 Hom.: 154

Bravo AF: 0.150

Asia WGS AF: 0.334 AC: 1157 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.46

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: rs4675826; hg19: chr2-242129831;