1-16160298-A-G

Variant names:

• chr1-16160298-A-G
• rs904106
• ENST00000426353.1:n.161+872A>G

Variant summary

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

The ENST00000426353.1(EPHA2-AS1):​n.161+872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,222 control chromosomes in the GnomAD database, including 58,337 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 (58337 hom., cov: 33)
• Consequence: EPHA2-AS1 ENST00000426353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 5 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=-0.84).
• 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: ENST00000426353.1. 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.751-1203A>G		intron	N/A
	EPHA2-AS1	NR_187273.1		n.750+3119A>G		intron	N/A
	EPHA2-AS1	NR_187275.1		n.750+3119A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA2-AS1	ENST00000426353.1	TSL:3	n.161+872A>G		intron	N/A
	EPHA2-AS1	ENST00000793379.1		n.526+4543A>G		intron	N/A
	EPHA2-AS1	ENST00000793381.1		n.274+872A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131903 AN: 152104 Hom.: 58322 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.867 AC: 131963 AN: 152222 Hom.: 58337 Cov.: 33 AF XY: 0.868 AC XY: 64627 AN XY: 74426

African (AFR) AF: 0.673 AC: 27917 AN: 41482

American (AMR) AF: 0.921 AC: 14093 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3243 AN: 3472

East Asian (EAS) AF: 0.893 AC: 4624 AN: 5180

South Asian (SAS) AF: 0.897 AC: 4329 AN: 4824

European-Finnish (FIN) AF: 0.967 AC: 10263 AN: 10612

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64434 AN: 68034

Other (OTH) AF: 0.894 AC: 1892 AN: 2116

Alfa AF: 0.923 Hom.: 250435

Bravo AF: 0.856

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.83
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs904106; hg19: chr1-16486793;