chr2-241191524-T-A

Position:

• chr2-241191524-T-A

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.166+273T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,100 control chromosomes in the GnomAD database, including 8,267 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (8267 hom., cov: 32)
• Consequence: ANO7 NM_001370694.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.284

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=-0.83).
• BP6: Variant 2-241191524-T-A is Benign according to our data. Variant chr2-241191524-T-A is described in ClinVar as [Benign]. Clinvar id is 1267835.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2	c.166+273T>A		intron_variant		ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000674324.2	c.166+273T>A		intron_variant			NM_001370694.2	A2
ANO7	ENST00000274979.12	c.328+273T>A		intron_variant		1		P2
ANO7	ENST00000402530.8	c.166+273T>A		intron_variant		1
ANO7	ENST00000402430.8	c.166+273T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44412 AN: 151982 Hom.: 8271 Cov.: 32

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.292 AC: 44399 AN: 152100 Hom.: 8267 Cov.: 32 AF XY: 0.289 AC XY: 21487 AN XY: 74354

Gnomad4 AFR AF: 0.0846

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.331

Alfa AF: 0.351 Hom.: 1296

Bravo AF: 0.278

Asia WGS AF: 0.156 AC: 546 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 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.79

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: rs2074837; hg19: chr2-242130939;