rs6603883

chr1-16156481-A-Gchr1-16156481-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424774.2(EPHA2-AS1):n.581-490A>G variant causes a intron, non coding transcript 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 ENST00000424774.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
EPHA2-AS1	XR_007065487.1	n.542-490A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHA2-AS1	ENST00000424774.2	n.581-490A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.595

Alfa AF: 0.606 Hom.: 27555

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

Splicing

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

Publications

LitVar

Other links and lift over

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