rs2856329

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001987.5(ETV6):​c.163+37207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,976 control chromosomes in the GnomAD database, including 11,498 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 0.37 ( 11498 hom., cov: 32)

Consequence

ETV6
NM_001987.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.606
Variant links:
Genes affected
ETV6 (HGNC:3495): (ETS variant transcription factor 6) This gene encodes an ETS family transcription factor. The product of this gene contains two functional domains: a N-terminal pointed (PNT) domain that is involved in protein-protein interactions with itself and other proteins, and a C-terminal DNA-binding domain. Gene knockout studies in mice suggest that it is required for hematopoiesis and maintenance of the developing vascular network. This gene is known to be involved in a large number of chromosomal rearrangements associated with leukemia and congenital fibrosarcoma. [provided by RefSeq, Sep 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ETV6NM_001987.5 linkuse as main transcriptc.163+37207C>T intron_variant ENST00000396373.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ETV6ENST00000396373.9 linkuse as main transcriptc.163+37207C>T intron_variant 1 NM_001987.5 P1
ETV6ENST00000545027.1 linkuse as main transcriptc.79+37207C>T intron_variant 5
ETV6ENST00000541426.1 linkuse as main transcriptn.348-35858C>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.372
AC:
56452
AN:
151856
Hom.:
11477
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.527
Gnomad AMI
AF:
0.438
Gnomad AMR
AF:
0.468
Gnomad ASJ
AF:
0.377
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.248
Gnomad FIN
AF:
0.281
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.380
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.372
AC:
56537
AN:
151976
Hom.:
11498
Cov.:
32
AF XY:
0.369
AC XY:
27446
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.528
Gnomad4 AMR
AF:
0.468
Gnomad4 ASJ
AF:
0.377
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.249
Gnomad4 FIN
AF:
0.281
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.379
Alfa
AF:
0.322
Hom.:
7594
Bravo
AF:
0.395
Asia WGS
AF:
0.216
AC:
755
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.0
DANN
Benign
0.48

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.

Other links and lift over

dbSNP: rs2856329; hg19: chr12-11942720; API