Genetic Variant ETS2-AS1:n.742-5159A>G (chr21-38885531-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000380931.6(ETS2-AS1):n.742-5159A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,208 control chromosomes in the GnomAD database, including 731 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 0.093 ( 731 hom., cov: 33)

Consequence

ETS2-AS1
ENST00000380931.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379

Publications

2 publications found

Variant links:

Genes affected

ETS2-AS1 (HGNC:56712): (ETS2 antisense RNA 1)

ETS2-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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETS2-AS1	NR_120405.1 link	n.742-5159A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ETS2-AS1	ENST00000380931.6 link	n.742-5159A>G	intron_variant	Intron 3 of 3	2
ETS2-AS1	ENST00000415824.1 link	n.342-5159A>G	intron_variant	Intron 3 of 3	5
ETS2-AS1	ENST00000626259.2 link	n.223+16370A>G	intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0924

AC:

14049

AN:

152090

Hom.:

725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.0520

Gnomad ASJ

AF:

0.0409

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0257

Gnomad FIN

AF:

0.0715

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0953

Gnomad OTH

AF:

0.0693

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

GnomAD4 genome

AF:

0.0925

AC:

14084

AN:

152208

Hom.:

731

Cov.:

AF XY:

0.0890

AC XY:

6622

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.132

AC:

5469

AN:

41494

American (AMR)

AF:

0.0520

AC:

796

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0409

AC:

142

AN:

3470

East Asian (EAS)

AF:

0.00251

AC:

AN:

5180

South Asian (SAS)

AF:

0.0257

AC:

124

AN:

4826

European-Finnish (FIN)

AF:

0.0715

AC:

758

AN:

10596

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0953

AC:

6483

AN:

68024

Other (OTH)

AF:

0.0686

AC:

145

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

650

1300

1949

2599

3249

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.0908

Hom.:

341

Bravo

AF:

0.0914

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.56

PhyloP100

-0.38

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