chr2-241190138-G-C

Variant names:

• chr2-241190138-G-C
• rs150023062
• NM_001370694.2:c.75G>C

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001370694.2(ANO7):​c.75G>C​(p.Arg25Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,573,580 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0011 (1 hom., cov: 33)
  • Exomes 𝑓: 0.000098 (1 hom.)
• Consequence: ANO7 NM_001370694.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.90
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.004346609).
• BP6: Variant 2-241190138-G-C is Benign according to our data. Variant chr2-241190138-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 767880.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370694.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO7	NM_001370694.2	MANE Select	c.75G>C	p.Arg25Ser	missense	Exon 2 of 25	NP_001357623.1	A0A6I8PRE6
	ANO7	NM_001001666.4		c.75G>C	p.Arg25Ser	missense	Exon 2 of 4	NP_001001666.2	A0A6Q8JT31

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANO7	ENST00000674324.2	MANE Select	c.75G>C	p.Arg25Ser	missense	Exon 2 of 25	ENSP00000501393.1	A0A6I8PRE6
	ANO7	ENST00000274979.12	TSL:1	c.237G>C	p.Arg79Ser	missense	Exon 2 of 25	ENSP00000274979.8	Q6IWH7-1
	ANO7	ENST00000402530.8	TSL:1	c.75G>C	p.Arg25Ser	missense	Exon 2 of 4	ENSP00000383985.4	A0A6Q8JT31

Frequencies

GnomAD3 genomes AF: 0.00108 AC: 164 AN: 152142 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00377

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000523

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000260 AC: 48 AN: 184456 AF XY: 0.000213

Gnomad AFR exome AF: 0.00361

Gnomad AMR exome AF: 0.000330

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000978 AC: 139 AN: 1421320 Hom.: 1 Cov.: 31 AF XY: 0.0000896 AC XY: 63 AN XY: 703122

African (AFR) AF: 0.00345 AC: 113 AN: 32716

American (AMR) AF: 0.000311 AC: 12 AN: 38572

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25354

East Asian (EAS) AF: 0.00 AC: 0 AN: 37558

South Asian (SAS) AF: 0.00 AC: 0 AN: 80730

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50086

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5712

European-Non Finnish (NFE) AF: 0.00000183 AC: 2 AN: 1091678

Other (OTH) AF: 0.000204 AC: 12 AN: 58914

GnomAD4 genome AF: 0.00108 AC: 164 AN: 152260 Hom.: 1 Cov.: 33 AF XY: 0.00111 AC XY: 83 AN XY: 74444

African (AFR) AF: 0.00376 AC: 156 AN: 41538

American (AMR) AF: 0.000523 AC: 8 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68008

Other (OTH) AF: 0.00 AC: 0 AN: 2110

Alfa AF: 0.000140 Hom.: 0

Bravo AF: 0.00110

ESP6500AA AF: 0.00204 AC: 9

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000244 AC: 29

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.51	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	0.13
DANN	Benign	0.58
DEOGEN2	Benign	0.028	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.022	N
LIST_S2	Benign	0.41	T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.0043	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		-1.9
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-1.7	N
REVEL	Benign	0.072
Sift	Benign	0.53	T
Sift4G	Benign	0.14	T
Polyphen		0.19	B
Vest4		0.10
MutPred		0.28		Gain of glycosylation at R79 (P = 0.0015)
MVP		0.16
MPC		0.12
ClinPred		0.0073	T
GERP RS		-2.3
Varity_R		0.096
gMVP		0.20
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs150023062; hg19: chr2-242129553;