rs904106

Positions:

• chr1-16160298-A-G
• chr1-16160298-A-T

Variant summary

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

The XR_007065487.1(EPHA2-AS1):​n.3869A>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 0.867 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 XR_007065487.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

EPHA2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA2-AS1	XR_007065487.1	n.3869A>G		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000426353.1	n.161+872A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.894

Alfa AF: 0.936 Hom.: 109636

Bravo AF: 0.856

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904106; hg19: chr1-16486793;