chr2-241190354-T-G

Position:

• chr2-241190354-T-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.108+183T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,024 control chromosomes in the GnomAD database, including 8,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.33 (8434 hom., cov: 32)
• Consequence: ANO7 NM_001370694.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.52

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=-0.93).
• BP6: Variant 2-241190354-T-G is Benign according to our data. Variant chr2-241190354-T-G is described in ClinVar as [Benign]. Clinvar id is 1264627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANO7	NM_001370694.2	c.108+183T>G		intron_variant		ENST00000674324.2	NP_001357623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO7	ENST00000674324.2	c.108+183T>G		intron_variant			NM_001370694.2	ENSP00000501393	A2
ANO7	ENST00000274979.12	c.270+183T>G		intron_variant		1		ENSP00000274979	P2
ANO7	ENST00000402530.8	c.108+183T>G		intron_variant		1		ENSP00000383985
ANO7	ENST00000402430.8	c.108+183T>G		intron_variant		5		ENSP00000385418

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49690 AN: 151906 Hom.: 8423 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.327 AC: 49733 AN: 152024 Hom.: 8434 Cov.: 32 AF XY: 0.332 AC XY: 24672 AN XY: 74302

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.326

Alfa AF: 0.166 Hom.: 324

Bravo AF: 0.338

Asia WGS AF: 0.346 AC: 1201 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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs4675985; hg19: chr2-242129769;