Genetic Variant ENST00000429289.5:n.207-26975A>G (chr7-143477799-A-G) – 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.207-26975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,443,876 control chromosomes in the GnomAD database, including 420,977 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 0.78 ( 46242 hom., cov: 29)

Exomes 𝑓: 0.76 ( 374735 hom. )

Consequence

EPHA1-AS1
ENST00000429289.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510

Publications

12 publications found

Variant links:

COSMIC-nc: COSV68765264

Genes affected

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

EPHA1-AS1 links:

TAS2R41 (HGNC:18883): (taste 2 receptor member 41) This gene encodes a member of the bitter taste receptor family which belong to the G protein-coupled receptor superfamily and are predominantly expressed in taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a seven-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered together with eight other taste receptor genes on chromosome 7. Chloramphenicol is an agonist for the encoded protein. [provided by RefSeq, Jul 2017]

TAS2R41 links:

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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 = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429289.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA1-AS1	NR_033897.1		n.207-26975A>G		intron	N/A
	TAS2R41	NM_176883.2	MANE Select	c.-74A>G		upstream_gene	N/A	NP_795364.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
EPHA1-AS1	ENST00000429289.5	TSL:1	n.207-26975A>G	intron	N/A
EPHA1-AS1	ENST00000690912.2		n.228-18167A>G	intron	N/A
EPHA1-AS1	ENST00000703017.1		n.206-18167A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.777

AC:

117998

AN:

151844

Hom.:

46198

Cov.:

show subpopulations

Gnomad AFR

AF:

0.847

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.748

Gnomad ASJ

AF:

0.756

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.772

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.764

Gnomad OTH

AF:

0.788

GnomAD4 exome

AF:

0.761

AC:

982632

AN:

1291914

Hom.:

374735

AF XY:

0.759

AC XY:

490864

AN XY:

646898

show subpopulations

African (AFR)

AF:

0.854

AC:

25782

AN:

30202

American (AMR)

AF:

0.735

AC:

31584

AN:

42950

Ashkenazi Jewish (ASJ)

AF:

0.761

AC:

17420

AN:

22892

East Asian (EAS)

AF:

0.620

AC:

24015

AN:

38748

South Asian (SAS)

AF:

0.709

AC:

54685

AN:

77182

European-Finnish (FIN)

AF:

0.764

AC:

39148

AN:

51270

Middle Eastern (MID)

AF:

0.752

AC:

3236

AN:

4304

European-Non Finnish (NFE)

AF:

0.769

AC:

745609

AN:

970032

Other (OTH)

AF:

0.757

AC:

41153

AN:

54334

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

12248

24497

36745

48994

61242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17232

34464

51696

68928

86160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.777

AC:

118102

AN:

151962

Hom.:

46242

Cov.:

AF XY:

0.774

AC XY:

57495

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.847

AC:

35130

AN:

41460

American (AMR)

AF:

0.748

AC:

11424

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.756

AC:

2622

AN:

3468

East Asian (EAS)

AF:

0.622

AC:

3195

AN:

5134

South Asian (SAS)

AF:

0.687

AC:

3297

AN:

4802

European-Finnish (FIN)

AF:

0.772

AC:

8149

AN:

10558

Middle Eastern (MID)

AF:

0.738

AC:

217

AN:

294

European-Non Finnish (NFE)

AF:

0.764

AC:

51904

AN:

67954

Other (OTH)

AF:

0.790

AC:

1665

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1345

2689

4034

5378

6723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.764

Hom.:

22966

Bravo

AF:

0.780

Asia WGS

AF:

0.692

AC:

2408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.7

(source)

DANN

Benign

0.74

PhyloP100

-0.051

PromoterAI

-0.0010

Neutral

(source)

Mutation Taster

=14/86

disease causing

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over