NM_001099667.3:c.298-829C>T

Variant names:

• chr10-122456078-C-T
• rs2736912
• NM_001099667.3:c.298-829C>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.298-829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,836 control chromosomes in the GnomAD database, including 1,482 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1482 hom., cov: 31)
• Consequence: ARMS2 NM_001099667.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 13 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099667.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMS2	NM_001099667.3	MANE Select	c.298-829C>T		intron	N/A	NP_001093137.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMS2	ENST00000528446.1	TSL:1 MANE Select	c.298-829C>T		intron	N/A	ENSP00000436682.1
	ENSG00000285955	ENST00000647969.1		n.182+2417G>A		intron	N/A
	ENSG00000285955	ENST00000650300.1		n.1852+2417G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19899 AN: 151718 Hom.: 1479 Cov.: 31

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.131 AC: 19919 AN: 151836 Hom.: 1482 Cov.: 31 AF XY: 0.130 AC XY: 9619 AN XY: 74174

African (AFR) AF: 0.0757 AC: 3136 AN: 41426

American (AMR) AF: 0.131 AC: 1999 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3464

East Asian (EAS) AF: 0.162 AC: 838 AN: 5160

South Asian (SAS) AF: 0.0674 AC: 324 AN: 4804

European-Finnish (FIN) AF: 0.171 AC: 1797 AN: 10502

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10934 AN: 67930

Other (OTH) AF: 0.138 AC: 290 AN: 2098

Alfa AF: 0.148 Hom.: 6512

Bravo AF: 0.124

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.020
DANN	Benign	0.35
PhyloP100		-2.5
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: rs2736912; hg19: chr10-124215594;