rs3750847

chr10-122455905-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ARMS2	NM_001099667.3	c.297+881C>T		intron_variant		ENST00000528446.1
LOC105378525	XR_946382.3	n.1874+2590G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMS2	ENST00000528446.1	c.297+881C>T		intron_variant		1	NM_001099667.3	P1
	ENST00000650300.1	n.1852+2590G>A		intron_variant, non_coding_transcript_variant
	ENST00000647969.1	n.182+2590G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.232

Alfa AF: 0.248 Hom.: 8821

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

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs3750847; hg19: chr10-124215421;