rs904107

Variant names:

• chr1-16162328-A-G
• rs904107
• NR_187272.1:n.1578A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187272.1(EPHA2-AS1):​n.1578A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,218 control chromosomes in the GnomAD database, including 58,614 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 0.87 (58614 hom., cov: 32)
• Consequence: EPHA2-AS1 NR_187272.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 2 publications found

Genes affected

EPHA2-AS1 (HGNC:40216): (EPHA2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187272.1. 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
	EPHA2-AS1	NR_187272.1		n.1578A>G		non_coding_transcript_exon	Exon 3 of 3
	EPHA2-AS1	NR_187273.1		n.751-2143A>G		intron	N/A
	EPHA2-AS1	NR_187275.1		n.751-2428A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA2-AS1	ENST00000793379.1		n.527-5848A>G		intron	N/A
	EPHA2-AS1	ENST00000793381.1		n.274+2902A>G		intron	N/A
	EPHA2-AS1	ENST00000793382.1		n.287-2143A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132270 AN: 152100 Hom.: 58594 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.869 AC: 132338 AN: 152218 Hom.: 58614 Cov.: 32 AF XY: 0.871 AC XY: 64791 AN XY: 74424

African (AFR) AF: 0.681 AC: 28246 AN: 41490

American (AMR) AF: 0.923 AC: 14123 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3239 AN: 3468

East Asian (EAS) AF: 0.893 AC: 4621 AN: 5176

South Asian (SAS) AF: 0.898 AC: 4334 AN: 4824

European-Finnish (FIN) AF: 0.967 AC: 10269 AN: 10616

Middle Eastern (MID) AF: 0.959 AC: 280 AN: 292

European-Non Finnish (NFE) AF: 0.947 AC: 64441 AN: 68026

Other (OTH) AF: 0.898 AC: 1899 AN: 2114

Alfa AF: 0.906 Hom.: 9507

Bravo AF: 0.859

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.66
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs904107; hg19: chr1-16488823;