rs61544945

Positions:

• chr10-122455084-G-GGT

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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:):

ACMG classification

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	c.297+62_297+63dupTG		intron_variant		ENST00000528446.1	NP_001093137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMS2	ENST00000528446.1	c.297+62_297+63dupTG		intron_variant		1	NM_001099667.3	ENSP00000436682.1
ENSG00000285955	ENST00000647969.1	n.182+3409_182+3410dupAC		intron_variant
ENSG00000285955	ENST00000650300.1	n.1852+3409_1852+3410dupAC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35665 AN: 151862 Hom.: 4382 Cov.: 25

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

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.: 25 AF XY: 0.238 AC XY: 17651 AN XY: 74304

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61544945; hg19: chr10-124214600;