Genetic Variant ENST00000429289.5:n.74+2897C>T (chr7-143410783-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 ENST00000429289.5(EPHA1-AS1):n.74+2897C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,968 control chromosomes in the GnomAD database, including 3,383 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 0.21 ( 3383 hom., cov: 30)

Consequence

EPHA1-AS1
ENST00000429289.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

13 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1 link	n.74+2897C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EPHA1-AS1	ENST00000429289.5 link	n.74+2897C>T	intron_variant	Intron 1 of 4	1
EPHA1-AS1	ENST00000841079.1 link	n.26C>T	non_coding_transcript_exon_variant	Exon 1 of 3
EPHA1-AS1	ENST00000841080.1 link	n.20C>T	non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31207

AN:

151852

Hom.:

3374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.181

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

GnomAD4 genome

AF:

0.206

AC:

31244

AN:

151968

Hom.:

3383

Cov.:

AF XY:

0.202

AC XY:

15024

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.242

AC:

10011

AN:

41394

American (AMR)

AF:

0.195

AC:

2979

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

389

AN:

3472

East Asian (EAS)

AF:

0.147

AC:

761

AN:

5162

South Asian (SAS)

AF:

0.261

AC:

1255

AN:

4814

European-Finnish (FIN)

AF:

0.148

AC:

1566

AN:

10576

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.201

AC:

13658

AN:

67968

Other (OTH)

AF:

0.178

AC:

376

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1224

2448

3673

4897

6121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.199

Hom.:

11724

Bravo

AF:

0.208

Asia WGS

AF:

0.194

AC:

675

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

(source)

DANN

Benign

0.55

PhyloP100

-1.7

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