1-16169419-G-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.8365+1166G>T 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 0.857 in 152,036 control chromosomes in the GnomAD database, including 56,299 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 0.86 (56299 hom., cov: 30)
• Consequence: EPHA2-AS1 XR_007065487.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

Genes affected

EPHA2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA2-AS1	XR_007065487.1	n.8365+1166G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130145 AN: 151918 Hom.: 56258 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.857 AC: 130242 AN: 152036 Hom.: 56299 Cov.: 30 AF XY: 0.854 AC XY: 63479 AN XY: 74298

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.882

Alfa AF: 0.875 Hom.: 5982

Bravo AF: 0.854

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.0
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4661717; hg19: chr1-16495914;