Variant 10-122455084-G-GGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001099667.3(ARMS2):c.297+62_297+63dupTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 937,644 control chromosomes in the GnomAD database, including 25,076 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 4389 hom., cov: 25)

Exomes 𝑓: 0.21 ( 20687 hom. )

Consequence

ARMS2
NM_001099667.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Variant links:

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]

ARMS2 links:

ENSG00000285955 (HGNC:):

ENSG00000285955 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMS2	NM_001099667.3 linkuse as main transcript	c.297+62_297+63dupTG		intron_variant		ENST00000528446.1	NP_001093137.1	P0C7Q2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ARMS2	ENST00000528446.1 linkuse as main transcript	c.297+62_297+63dupTG	intron_variant	1	NM_001099667.3	ENSP00000436682.1	P0C7Q2
ENSG00000285955	ENST00000647969.1 linkuse as main transcript	n.182+3409_182+3410dupAC	intron_variant
ENSG00000285955	ENST00000650300.1 linkuse as main transcript	n.1852+3409_1852+3410dupAC	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35665

AN:

151862

Hom.:

4382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.214

AC:

168255

AN:

785664

Hom.:

20687

AF XY:

0.217

AC XY:

87517

AN XY:

402836

show subpopulations

Gnomad4 AFR exome

AF:

0.220

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.192

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.304

Gnomad4 FIN exome

AF:

0.230

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.235

AC:

35705

AN:

151980

Hom.:

4389

Cov.:

AF XY:

0.238

AC XY:

17651

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.233

Gnomad4 ASJ

AF:

0.204

Gnomad4 EAS

AF:

0.413

Gnomad4 SAS

AF:

0.320

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.219

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.246

Hom.:

556

Bravo

AF:

0.236

Asia WGS

AF:

0.369

AC:

1278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over