10-122455905-C-T

Variant names:

• chr10-122455905-C-T
• rs3750847
• NM_001099667.3:c.297+881C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001099667.3(ARMS2):​c.297+881C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,862 control chromosomes in the GnomAD database, including 4,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.24 (4407 hom., cov: 32)
• Consequence: ARMS2 NM_001099667.3 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.550
• Publications: 30 publications found

Genes affected

ARMS2 (HGNC:32685): (age-related maculopathy susceptibility 2) This gene encodes a small secreted protein specific to primates. This protein is a component of the choroidal extracellular matrix of the eye. Mutations in this gene are associated with age-related macular degeneration. [provided by RefSeq, Sep 2017]

ENSG00000285955 (HGNC:58122):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMS2	NM_001099667.3	c.297+881C>T		intron_variant	Intron 1 of 1	ENST00000528446.1	NP_001093137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMS2	ENST00000528446.1	c.297+881C>T		intron_variant	Intron 1 of 1	1	NM_001099667.3	ENSP00000436682.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35669 AN: 151744 Hom.: 4400 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.235 AC: 35709 AN: 151862 Hom.: 4407 Cov.: 32 AF XY: 0.238 AC XY: 17651 AN XY: 74188

African (AFR) AF: 0.231 AC: 9585 AN: 41424

American (AMR) AF: 0.233 AC: 3551 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2134 AN: 5144

South Asian (SAS) AF: 0.320 AC: 1520 AN: 4756

European-Finnish (FIN) AF: 0.236 AC: 2483 AN: 10538

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14916 AN: 67956

Other (OTH) AF: 0.232 AC: 490 AN: 2110

Alfa AF: 0.244 Hom.: 9947

Bravo AF: 0.237

Asia WGS AF: 0.369 AC: 1279 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

-

Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.63
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs3750847; hg19: chr10-124215421;