dbSNP rs1700488: EPIST:n.487C>T (chr5-135039187-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 ENST00000507035.2(EPIST):n.487C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,260 control chromosomes in the GnomAD database, including 4,598 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 0.20 ( 4598 hom., cov: 33)

Exomes 𝑓: 0.061 ( 0 hom. )

Consequence

EPIST
ENST00000507035.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

Publications

1 publications found

Variant links:

Genes affected

EPIST (HGNC:49679): (esophagus epithelial intergenic associated transcript)

EPIST links:

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

PITX1-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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
EPIST	NR_105049.1 link	n.487C>T	non_coding_transcript_exon_variant	Exon 2 of 2
EPIST	NR_105050.1 link	n.482C>T	non_coding_transcript_exon_variant	Exon 2 of 2
PITX1-AS1	NR_161235.1 link	n.267+5647G>A	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EPIST	ENST00000507035.2 link	n.487C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
EPIST	ENST00000511256.2 link	n.228C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
EPIST	ENST00000807101.1 link	n.627C>T	non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30210

AN:

152076

Hom.:

4562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.0671

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.0497

Gnomad FIN

AF:

0.0756

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.191

GnomAD4 exome

AF:

0.0606

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0577

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0517

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.199

AC:

30319

AN:

152194

Hom.:

4598

Cov.:

AF XY:

0.192

AC XY:

14280

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.423

AC:

17563

AN:

41488

American (AMR)

AF:

0.207

AC:

3165

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0671

AC:

233

AN:

3472

East Asian (EAS)

AF:

0.00174

AC:

AN:

5174

South Asian (SAS)

AF:

0.0510

AC:

246

AN:

4824

European-Finnish (FIN)

AF:

0.0756

AC:

802

AN:

10610

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7856

AN:

68006

Other (OTH)

AF:

0.189

AC:

398

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1104

2208

3313

4417

5521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.134

Hom.:

729

Bravo

AF:

0.221

Asia WGS

AF:

0.0520

AC:

182

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.9

(source)

DANN

Benign

0.78

PhyloP100

0.28

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