rs2302054

Variant names:

• chr2-241190100-G-A
• rs2302054
• NM_001370694.2:c.37G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-241190100-G-A
• chr2-241190100-G-C
• chr2-241190100-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001370694.2(ANO7):​c.37G>A​(p.Val13Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 1,584,012 control chromosomes in the GnomAD database, including 7,769 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.051 (977 hom., cov: 32)
  • Exomes 𝑓: 0.031 (6792 hom.)
• Consequence: ANO7 NM_001370694.2 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.178
• Publications: 13 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: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=2.9236078E-4).
• BP6: Variant 2-241190100-G-A is Benign according to our data. Variant chr2-241190100-G-A is described in ClinVar as Benign. ClinVar VariationId is 1246662.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

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.37G>A	p.Val13Ile	missense	Exon 2 of 25	NP_001357623.1	A0A6I8PRE6
	ANO7	NM_001001666.4		c.37G>A	p.Val13Ile	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.37G>A	p.Val13Ile	missense	Exon 2 of 25	ENSP00000501393.1	A0A6I8PRE6
	ANO7	ENST00000274979.12	TSL:1	c.199G>A	p.Val67Ile	missense	Exon 2 of 25	ENSP00000274979.8	Q6IWH7-1
	ANO7	ENST00000402530.8	TSL:1	c.37G>A	p.Val13Ile	missense	Exon 2 of 4	ENSP00000383985.4	A0A6Q8JT31

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7704 AN: 152070 Hom.: 973 Cov.: 32

Gnomad AFR AF: 0.0271

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00462

Gnomad OTH AF: 0.0632

GnomAD2 exomes AF: 0.0947 AC: 19169 AN: 202344 AF XY: 0.0848

Gnomad AFR exome AF: 0.0268

Gnomad AMR exome AF: 0.295

Gnomad ASJ exome AF: 0.00322

Gnomad EAS exome AF: 0.454

Gnomad FIN exome AF: 0.0365

Gnomad NFE exome AF: 0.00459

Gnomad OTH exome AF: 0.0676

GnomAD4 exome AF: 0.0308 AC: 44055 AN: 1431824 Hom.: 6792 Cov.: 32 AF XY: 0.0310 AC XY: 21969 AN XY: 709384

African (AFR) AF: 0.0235 AC: 775 AN: 33046

American (AMR) AF: 0.290 AC: 11608 AN: 40070

Ashkenazi Jewish (ASJ) AF: 0.00184 AC: 47 AN: 25504

East Asian (EAS) AF: 0.471 AC: 17926 AN: 38076

South Asian (SAS) AF: 0.0769 AC: 6266 AN: 81526

European-Finnish (FIN) AF: 0.0354 AC: 1800 AN: 50796

Middle Eastern (MID) AF: 0.00910 AC: 52 AN: 5716

European-Non Finnish (NFE) AF: 0.00261 AC: 2863 AN: 1097788

Other (OTH) AF: 0.0458 AC: 2718 AN: 59302

GnomAD4 genome AF: 0.0507 AC: 7713 AN: 152188 Hom.: 977 Cov.: 32 AF XY: 0.0587 AC XY: 4366 AN XY: 74396

African (AFR) AF: 0.0270 AC: 1123 AN: 41530

American (AMR) AF: 0.192 AC: 2941 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2382 AN: 5148

South Asian (SAS) AF: 0.0948 AC: 458 AN: 4830

European-Finnish (FIN) AF: 0.0339 AC: 360 AN: 10614

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

European-Non Finnish (NFE) AF: 0.00462 AC: 314 AN: 67998

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0200 Hom.: 569

Bravo AF: 0.0647

TwinsUK AF: 0.00135 AC: 5

ALSPAC AF: 0.00363 AC: 14

ESP6500AA AF: 0.0266 AC: 117

ESP6500EA AF: 0.00385 AC: 33

ExAC AF: 0.0711 AC: 8519

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.66	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.97
DEOGEN2	Benign	0.029	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.059	N
LIST_S2	Benign	0.50	T
MetaRNN	Benign	0.00029	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.18
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-0.43	N
REVEL	Benign	0.036
Sift	Benign	0.15	T
Sift4G	Benign	0.11	T
Polyphen		0.71	P
Vest4		0.073
MPC		0.087
ClinPred		0.0011	T
GERP RS		0.53
Varity_R		0.030
gMVP		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2302054; hg19: chr2-242129515; COSMIC: COSV107289572;