chr1-16178825-A-G

Variant names:

• chr1-16178825-A-G
• rs1497406
• ENST00000793379.1:n.605-3724A>G

Variant summary

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

The ENST00000793379.1(EPHA2-AS1):​n.605-3724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,830 control chromosomes in the GnomAD database, including 19,304 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 0.47 (19304 hom., cov: 32)
• Consequence: EPHA2-AS1 ENST00000793379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 27 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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA2-AS1	ENST00000793379.1	n.605-3724A>G		intron_variant	Intron 2 of 2
EPHA2-AS1	ENST00000793381.1	n.353-3724A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71864 AN: 151710 Hom.: 19316 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.473 AC: 71850 AN: 151830 Hom.: 19304 Cov.: 32 AF XY: 0.475 AC XY: 35213 AN XY: 74162

African (AFR) AF: 0.222 AC: 9188 AN: 41478

American (AMR) AF: 0.434 AC: 6614 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3464

East Asian (EAS) AF: 0.766 AC: 3954 AN: 5160

South Asian (SAS) AF: 0.439 AC: 2110 AN: 4808

European-Finnish (FIN) AF: 0.687 AC: 7206 AN: 10492

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39372 AN: 67854

Other (OTH) AF: 0.470 AC: 993 AN: 2114

Alfa AF: 0.533 Hom.: 48913

Bravo AF: 0.449

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1497406; hg19: chr1-16505320;