2-241195442-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.167-261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,160 control chromosomes in the GnomAD database, including 51,891 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.83 (51891 hom., cov: 32)
• Consequence: ANO7 NM_001370694.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.357

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=-0.91).
• BP6: Variant 2-241195442-A-G is Benign according to our data. Variant chr2-241195442-A-G is described in ClinVar as [Benign]. Clinvar id is 1229920.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2	c.167-261A>G		intron_variant		ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000674324.2	c.167-261A>G		intron_variant			NM_001370694.2	A2
ANO7	ENST00000274979.12	c.329-261A>G		intron_variant		1		P2
ANO7	ENST00000402530.8	c.167-264A>G		intron_variant		1
ANO7	ENST00000402430.8	c.167-264A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125463 AN: 152042 Hom.: 51839 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.825 AC: 125568 AN: 152160 Hom.: 51891 Cov.: 32 AF XY: 0.828 AC XY: 61554 AN XY: 74382

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.851

Alfa AF: 0.821 Hom.: 6831

Bravo AF: 0.832

Asia WGS AF: 0.850 AC: 2953 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	-0.91
Cadd	Benign	1.4
Dann	Benign	0.73

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: rs12998792; hg19: chr2-242134857;