1-16169419-G-T

Variant names:

• chr1-16169419-G-T
• rs4661717
• ENST00000793379.1:n.604+1166G>T

Variant summary

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

The ENST00000793379.1(EPHA2-AS1):​n.604+1166G>T variant causes a intron 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 ENST00000793379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 3 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=-0.98).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA2-AS1	ENST00000793379.1	n.604+1166G>T		intron_variant	Intron 2 of 2
EPHA2-AS1	ENST00000793381.1	n.352+1166G>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.731 AC: 30274 AN: 41438

American (AMR) AF: 0.911 AC: 13919 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3036 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4375 AN: 5154

South Asian (SAS) AF: 0.841 AC: 4056 AN: 4820

European-Finnish (FIN) AF: 0.873 AC: 9226 AN: 10564

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62370 AN: 67992

Other (OTH) AF: 0.882 AC: 1859 AN: 2108

Alfa AF: 0.868 Hom.: 6184

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4661717; hg19: chr1-16495914;