2-241190030-A-G

Position:

• chr2-241190030-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001370694.2(ANO7):​c.-7-27A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,542,002 control chromosomes in the GnomAD database, including 190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0046 (18 hom., cov: 32)
  • Exomes 𝑓: 0.0044 (172 hom.)
• Consequence: ANO7 NM_001370694.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.740

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 2-241190030-A-G is Benign according to our data. Variant chr2-241190030-A-G is described in ClinVar as [Benign]. Clinvar id is 1273665.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.078 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2	c.-7-27A>G		intron_variant		ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000674324.2	c.-7-27A>G		intron_variant			NM_001370694.2	A2
ANO7	ENST00000274979.12	c.156-27A>G		intron_variant		1		P2
ANO7	ENST00000402530.8	c.-7-27A>G		intron_variant		1
ANO7	ENST00000402430.8	c.-7-27A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00456 AC: 692 AN: 151848 Hom.: 19 Cov.: 32

Gnomad AFR AF: 0.000339

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000917

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0848

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.000568

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.00289

GnomAD3 exomes AF: 0.0122 AC: 1932 AN: 158068 Hom.: 56 AF XY: 0.0133 AC XY: 1115 AN XY: 83844

Gnomad AFR exome AF: 0.000769

Gnomad AMR exome AF: 0.000449

Gnomad ASJ exome AF: 0.00940

Gnomad EAS exome AF: 0.0891

Gnomad SAS exome AF: 0.0322

Gnomad FIN exome AF: 0.000579

Gnomad NFE exome AF: 0.000388

Gnomad OTH exome AF: 0.00686

GnomAD4 exome AF: 0.00443 AC: 6159 AN: 1390036 Hom.: 172 Cov.: 27 AF XY: 0.00519 AC XY: 3564 AN XY: 686362

Gnomad4 AFR exome AF: 0.000379

Gnomad4 AMR exome AF: 0.000451

Gnomad4 ASJ exome AF: 0.0118

Gnomad4 EAS exome AF: 0.0742

Gnomad4 SAS exome AF: 0.0311

Gnomad4 FIN exome AF: 0.000636

Gnomad4 NFE exome AF: 0.000221

Gnomad4 OTH exome AF: 0.00765

GnomAD4 genome AF: 0.00456 AC: 693 AN: 151966 Hom.: 18 Cov.: 32 AF XY: 0.00556 AC XY: 413 AN XY: 74292

Gnomad4 AFR AF: 0.000338

Gnomad4 AMR AF: 0.000916

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0846

Gnomad4 SAS AF: 0.0339

Gnomad4 FIN AF: 0.000568

Gnomad4 NFE AF: 0.000368

Gnomad4 OTH AF: 0.00381

Alfa AF: 0.00201 Hom.: 0

Bravo AF: 0.00498

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.48

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: rs2302053; hg19: chr2-242129445;