chr2-241189851-C-T

Position:

• chr2-241189851-C-T

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.-7-206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,126 control chromosomes in the GnomAD database, including 4,390 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.23 (4390 hom., cov: 32)
• Consequence: ANO7 NM_001370694.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.916

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=-0.89).
• BP6: Variant 2-241189851-C-T is Benign according to our data. Variant chr2-241189851-C-T is described in ClinVar as [Benign]. Clinvar id is 1279620.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2	c.-7-206C>T		intron_variant		ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000674324.2	c.-7-206C>T		intron_variant			NM_001370694.2	A2
ANO7	ENST00000274979.12	c.156-206C>T		intron_variant		1		P2
ANO7	ENST00000402530.8	c.-7-206C>T		intron_variant		1
ANO7	ENST00000402430.8	c.-7-206C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34648 AN: 152008 Hom.: 4390 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.228 AC: 34659 AN: 152126 Hom.: 4390 Cov.: 32 AF XY: 0.226 AC XY: 16788 AN XY: 74376

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.231

Alfa AF: 0.262 Hom.: 1136

Bravo AF: 0.217

Asia WGS AF: 0.105 AC: 366 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	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.7
DANN	Benign	0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs11683690; hg19: chr2-242129266;