rs17623531

chr10-122455405-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+381C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 152,112 control chromosomes in the GnomAD database, including 860 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 0.093 (860 hom., cov: 32)
• Consequence: ARMS2 NM_001099667.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMS2	NM_001099667.3	c.297+381C>T		intron_variant		ENST00000528446.1
LOC105378525	XR_946382.3	n.1874+3090G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMS2	ENST00000528446.1	c.297+381C>T		intron_variant		1	NM_001099667.3	P1
	ENST00000650300.1	n.1852+3090G>A		intron_variant, non_coding_transcript_variant
	ENST00000647969.1	n.182+3090G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14166 AN: 151994 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.00654

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0931 AC: 14161 AN: 152112 Hom.: 860 Cov.: 32 AF XY: 0.0914 AC XY: 6796 AN XY: 74376

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.00675

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.110

Alfa AF: 0.121 Hom.: 1218

Bravo AF: 0.0880

Asia WGS AF: 0.0820 AC: 285 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.0
Dann	Benign	0.45

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: rs17623531; hg19: chr10-124214921;