dbSNP rs11771145: EPHA1-AS1:n.75-1399G>A (chr7-143413669-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000429289.5(EPHA1-AS1):n.75-1399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,954 control chromosomes in the GnomAD database, including 13,661 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 0.41 ( 13661 hom., cov: 32)

Consequence

EPHA1-AS1
ENST00000429289.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0380

Publications

138 publications found

Variant links:

Genes affected

EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

EPHA1-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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1 link	n.75-1399G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EPHA1-AS1	ENST00000429289.5 link	n.75-1399G>A	intron_variant	Intron 1 of 4	1
EPHA1-AS1	ENST00000421648.3 link	n.330-1399G>A	intron_variant	Intron 1 of 2	2
EPHA1-AS1	ENST00000690912.2 link	n.96-1399G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62877

AN:

151836

Hom.:

13638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.372

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

GnomAD4 genome

AF:

0.414

AC:

62936

AN:

151954

Hom.:

13661

Cov.:

AF XY:

0.415

AC XY:

30795

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.554

AC:

22944

AN:

41410

American (AMR)

AF:

0.366

AC:

5589

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1093

AN:

3468

East Asian (EAS)

AF:

0.517

AC:

2674

AN:

5174

South Asian (SAS)

AF:

0.314

AC:

1514

AN:

4822

European-Finnish (FIN)

AF:

0.380

AC:

4011

AN:

10552

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.351

AC:

23846

AN:

67946

Other (OTH)

AF:

0.375

AC:

792

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1814

3628

5443

7257

9071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

586

1172

1758

2344

2930

<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:

0.366

Hom.:

49071

Bravo

AF:

0.422

Asia WGS

AF:

0.418

AC:

1454

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.2

(source)

DANN

Benign

0.74

PhyloP100

-0.038

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