dbSNP rs6661012: EPHA2-AS1:n.604+5165C>T (chr1-16173418-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000793379.1(EPHA2-AS1):n.604+5165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,166 control chromosomes in the GnomAD database, including 7,359 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 0.29 ( 7359 hom., cov: 32)

Consequence

EPHA2-AS1
ENST00000793379.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

2 publications found

Variant links:

COSMIC-nc: COSV59927171

Genes affected

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

EPHA2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 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 link	n.604+5165C>T		intron_variant	Intron 2 of 2
EPHA2-AS1	ENST00000793381.1 link	n.352+5165C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44088

AN:

152048

Hom.:

7351

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.0866

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.290

AC:

44108

AN:

152166

Hom.:

7359

Cov.:

AF XY:

0.291

AC XY:

21616

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.150

AC:

6215

AN:

41546

American (AMR)

AF:

0.439

AC:

6714

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.408

AC:

1414

AN:

3468

East Asian (EAS)

AF:

0.0868

AC:

450

AN:

5186

South Asian (SAS)

AF:

0.408

AC:

1968

AN:

4824

European-Finnish (FIN)

AF:

0.256

AC:

2714

AN:

10586

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23495

AN:

67960

Other (OTH)

AF:

0.336

AC:

710

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1531

3062

4592

6123

7654

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.339

Hom.:

5330

Bravo

AF:

0.293

Asia WGS

AF:

0.276

AC:

959

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.7

(source)

DANN

Benign

0.72

PhyloP100

1.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over