10-122457305-GTGATAGGCATTAACTAAAATTAAATAAAAATTCAGATCATCCTTGCACTTGCTGCATTTCAAATGCTTGGCAGTCACATGTAGTTAGTGGCTACCCTCTTGGACAGCACAGATAGAGATTATTTCCATCACTGCAGAAAATTCTAGACTTTGAGCTTCTTGAGGACAGGGGCTTGATCATTCGACACTGCTTTACAGTGTCTAGCAGTGTCTACCCTGTGGCAGGGGCTCAGGAAATTTTTCCTGAACCGAACCTAACTGAACTGATGTGGGTTTGTCATCAGGGTGTACCTGCTGTTAAAGGAGGTTACGACCTCTGATGCTGGGGTGGCCAGAGGGGATGGGAGTGGGTCTGGCACTCTGAGGAAAGGGGGTGAAACCAGCTGAGAAGTCATCTTTTACCTGCTGGCATGGCCCCAGCCAGGGTTCTGTTGCTATGGGAGA-TTATTAATTAATTAACTAAAATTAAATTATTTAGTTAATTTAATTAACTAAACT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The 10-122457305-GTGATAGGCATTAACTAAAATTAAATAAAAATTCAGATCATCCTTGCACTTGCTGCATTTCAAATGCTTGGCAGTCACATGTAGTTAGTGGCTACCCTCTTGGACAGCACAGATAGAGATTATTTCCATCACTGCAGAAAATTCTAGACTTTGAGCTTCTTGAGGACAGGGGCTTGATCATTCGACACTGCTTTACAGTGTCTAGCAGTGTCTACCCTGTGGCAGGGGCTCAGGAAATTTTTCCTGAACCGAACCTAACTGAACTGATGTGGGTTTGTCATCAGGGTGTACCTGCTGTTAAAGGAGGTTACGACCTCTGATGCTGGGGTGGCCAGAGGGGATGGGAGTGGGTCTGGCACTCTGAGGAAAGGGGGTGAAACCAGCTGAGAAGTCATCTTTTACCTGCTGGCATGGCCCCAGCCAGGGTTCTGTTGCTATGGGAGA-TTATTAATTAATTAACTAAAATTAAATTATTTAGTTAATTTAATTAACTAAACT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: not found (cov: 25)
• Consequence: ARMS2 NM_001099667.3 3_prime_UTR
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 2.13

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMS2	NM_001099667.3			3_prime_UTR_variant	2/2	ENST00000528446.1
LOC105378525	XR_946382.3	n.1874+747_1874+1190delinsAGTTTAGTTAATTAAATTAACTAAATAATTTAATTTTAGTTAATTAATTAATAA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMS2	ENST00000528446.1			3_prime_UTR_variant	2/2	1	NM_001099667.3	P1
	ENST00000650300.1	n.1852+747_1852+1190delinsAGTTTAGTTAATTAAATTAACTAAATAATTTAATTTTAGTTAATTAATTAATAA		intron_variant, non_coding_transcript_variant
	ENST00000647969.1	n.182+747_182+1190delinsAGTTTAGTTAATTAAATTAACTAAATAATTTAATTTTAGTTAATTAATTAATAA		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 25

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

GnomAD4 genome Cov.: 25

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Age related macular degeneration 8 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jul 01, 2008

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-124216821;