rs6603883

Variant names:

• chr1-16156481-A-G
• rs6603883
• ENST00000424774.3:n.685-490A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-16156481-A-G
• chr1-16156481-A-T

Variant summary

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

The ENST00000424774.3(EPHA2-AS1):​n.685-490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,088 control chromosomes in the GnomAD database, including 29,103 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 0.61 (29103 hom., cov: 33)
• Consequence: EPHA2-AS1 ENST00000424774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 12 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA2-AS1	NR_187272.1	n.542-490A>G		intron_variant	Intron 1 of 2
EPHA2-AS1	NR_187273.1	n.542-490A>G		intron_variant	Intron 1 of 2
EPHA2-AS1	NR_187274.1	n.542-490A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA2-AS1	ENST00000424774.3	n.685-490A>G		intron_variant	Intron 1 of 1	2
EPHA2-AS1	ENST00000793379.1	n.526+726A>G		intron_variant	Intron 1 of 2
EPHA2-AS1	ENST00000793382.1	n.78-490A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93459 AN: 151970 Hom.: 29078 Cov.: 33

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.615 AC: 93529 AN: 152088 Hom.: 29103 Cov.: 33 AF XY: 0.617 AC XY: 45885 AN XY: 74352

African (AFR) AF: 0.603 AC: 25018 AN: 41464

American (AMR) AF: 0.568 AC: 8688 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1807 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4639 AN: 5180

South Asian (SAS) AF: 0.575 AC: 2768 AN: 4810

European-Finnish (FIN) AF: 0.689 AC: 7291 AN: 10576

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41330 AN: 67976

Other (OTH) AF: 0.595 AC: 1256 AN: 2112

Alfa AF: 0.609 Hom.: 41412

Bravo AF: 0.611

Asia WGS AF: 0.699 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.4
DANN	Benign	0.81
PhyloP100		0.093
PromoterAI		0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6603883; hg19: chr1-16482976; COSMIC: COSV64452925;