chr12-11822598-T-C

Variant summary

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

The NM_001987.5(ETV6):​c.164-16542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,180 control chromosomes in the GnomAD database, including 42,382 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 ( 42382 hom., cov: 32)

Consequence

ETV6
NM_001987.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.758
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ETV6NM_001987.5 linkuse as main transcriptc.164-16542T>C intron_variant ENST00000396373.9 NP_001978.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ETV6ENST00000396373.9 linkuse as main transcriptc.164-16542T>C intron_variant 1 NM_001987.5 ENSP00000379658 P1
ETV6ENST00000545027.1 linkuse as main transcriptc.80-16542T>C intron_variant 5 ENSP00000441463
ETV6ENST00000541426.1 linkuse as main transcriptn.348-3046T>C intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.736
AC:
111866
AN:
152062
Hom.:
42329
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.923
Gnomad AMI
AF:
0.698
Gnomad AMR
AF:
0.624
Gnomad ASJ
AF:
0.674
Gnomad EAS
AF:
0.736
Gnomad SAS
AF:
0.682
Gnomad FIN
AF:
0.752
Gnomad MID
AF:
0.672
Gnomad NFE
AF:
0.652
Gnomad OTH
AF:
0.722
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.736
AC:
111976
AN:
152180
Hom.:
42382
Cov.:
32
AF XY:
0.735
AC XY:
54687
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.923
Gnomad4 AMR
AF:
0.624
Gnomad4 ASJ
AF:
0.674
Gnomad4 EAS
AF:
0.736
Gnomad4 SAS
AF:
0.683
Gnomad4 FIN
AF:
0.752
Gnomad4 NFE
AF:
0.652
Gnomad4 OTH
AF:
0.721
Alfa
AF:
0.669
Hom.:
20350
Bravo
AF:
0.739
Asia WGS
AF:
0.709
AC:
2467
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
20
DANN
Benign
0.64

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: rs2710287; hg19: chr12-11975532; API