Variant 21-38819507-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005239.6(ETS2):c.816T>G(p.Thr272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 1,612,886 control chromosomes in the GnomAD database, including 524,442 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 0.74 ( 42850 hom., cov: 31)

Exomes 𝑓: 0.80 ( 481592 hom. )

Consequence

ETS2
NM_005239.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0880

Variant links:

Genes affected

ETS2 (HGNC:3489): (ETS proto-oncogene 2, transcription factor) This gene encodes a transcription factor which regulates genes involved in development and apoptosis. The encoded protein is also a protooncogene and shown to be involved in regulation of telomerase. A pseudogene of this gene is located on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ETS2 links:

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

ETS2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-0.088 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ETS2	NM_005239.6 linkuse as main transcript	c.816T>G	p.Thr272=	synonymous_variant	8/10	ENST00000360938.8	NP_005230.1
ETS2	NM_001256295.2 linkuse as main transcript	c.1236T>G	p.Thr412=	synonymous_variant	9/11		NP_001243224.1
ETS2	XM_005260935.2 linkuse as main transcript	c.816T>G	p.Thr272=	synonymous_variant	8/10		XP_005260992.1
ETS2	XM_017028290.2 linkuse as main transcript	c.816T>G	p.Thr272=	synonymous_variant	8/10		XP_016883779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ETS2	ENST00000360938.8 linkuse as main transcript	c.816T>G	p.Thr272=	synonymous_variant	8/10	1	NM_005239.6	ENSP00000354194	P1
ETS2-AS1	ENST00000663561.1 linkuse as main transcript	n.535-6082A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.739

AC:

112285

AN:

151874

Hom.:

42851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.616

Gnomad AMI

AF:

0.904

Gnomad AMR

AF:

0.686

Gnomad ASJ

AF:

0.865

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.507

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.853

Gnomad OTH

AF:

0.758

GnomAD3 exomes

AF:

0.718

AC:

179825

AN:

250562

Hom.:

67698

AF XY:

0.719

AC XY:

97420

AN XY:

135522

show subpopulations

Gnomad AFR exome

AF:

0.607

Gnomad AMR exome

AF:

0.564

Gnomad ASJ exome

AF:

0.853

Gnomad EAS exome

AF:

0.472

Gnomad SAS exome

AF:

0.524

Gnomad FIN exome

AF:

0.752

Gnomad NFE exome

AF:

0.852

Gnomad OTH exome

AF:

0.772

GnomAD4 exome

AF:

0.803

AC:

1173544

AN:

1460894

Hom.:

481592

Cov.:

AF XY:

0.796

AC XY:

578596

AN XY:

726650

show subpopulations

Gnomad4 AFR exome

AF:

0.598

Gnomad4 AMR exome

AF:

0.576

Gnomad4 ASJ exome

AF:

0.851

Gnomad4 EAS exome

AF:

0.450

Gnomad4 SAS exome

AF:

0.529

Gnomad4 FIN exome

AF:

0.754

Gnomad4 NFE exome

AF:

0.855

Gnomad4 OTH exome

AF:

0.778

GnomAD4 genome

AF:

0.739

AC:

112313

AN:

151992

Hom.:

42850

Cov.:

AF XY:

0.728

AC XY:

54115

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.615

Gnomad4 AMR

AF:

0.685

Gnomad4 ASJ

AF:

0.865

Gnomad4 EAS

AF:

0.459

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.749

Gnomad4 NFE

AF:

0.853

Gnomad4 OTH

AF:

0.754

Alfa

AF:

0.824

Hom.:

85678

Bravo

AF:

0.732

Asia WGS

AF:

0.495

AC:

1722

AN:

3478

EpiCase

AF:

0.840

EpiControl

AF:

0.848

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.1

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over