10-122455460-G-T

Variant names:

• chr10-122455460-G-T
• rs36212731
• NM_001099667.3:c.297+436G>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+436G>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 151,904 control chromosomes in the GnomAD database, including 4,413 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 0.24 (4413 hom., cov: 32)
• Consequence: ARMS2 NM_001099667.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 9 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]

HTRA1-AS1 (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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMS2	NM_001099667.3	MANE Select	c.297+436G>T		intron	N/A	NP_001093137.1	P0C7Q2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMS2	ENST00000528446.1	TSL:1 MANE Select	c.297+436G>T		intron	N/A	ENSP00000436682.1	P0C7Q2
	HTRA1-AS1	ENST00000647969.1		n.182+3035C>A		intron	N/A
	HTRA1-AS1	ENST00000650300.1		n.1852+3035C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35697 AN: 151786 Hom.: 4406 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: 0.188

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.235 AC: 35737 AN: 151904 Hom.: 4413 Cov.: 32 AF XY: 0.238 AC XY: 17666 AN XY: 74256

African (AFR) AF: 0.232 AC: 9586 AN: 41400

American (AMR) AF: 0.233 AC: 3560 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3466

East Asian (EAS) AF: 0.414 AC: 2136 AN: 5154

South Asian (SAS) AF: 0.319 AC: 1531 AN: 4800

European-Finnish (FIN) AF: 0.236 AC: 2487 AN: 10536

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14916 AN: 67970

Other (OTH) AF: 0.233 AC: 492 AN: 2108

Alfa AF: 0.139 Hom.: 279

Bravo AF: 0.237

Asia WGS AF: 0.369 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.036
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: rs36212731; hg19: chr10-124214976;