chr12-11725530-C-A

Variant names:

• chr12-11725530-C-A
• rs2900208
• NM_001987.5:c.34-26920C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001987.5(ETV6):​c.34-26920C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,900 control chromosomes in the GnomAD database, including 6,930 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 0.29 (6930 hom., cov: 31)
• Consequence: ETV6 NM_001987.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 10 publications found

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]

ETV6 Gene-Disease associations (from GenCC):

• thrombocytopenia 5

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
• acute myeloid leukemia

  Inheritance: AD, Unknown Classification: STRONG, LIMITED Submitted by: Genomics England PanelApp, Ambry Genetics
• hereditary thrombocytopenia and hematologic cancer predisposition syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETV6	NM_001987.5	c.34-26920C>A		intron_variant	Intron 1 of 7	ENST00000396373.9	NP_001978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETV6	ENST00000396373.9	c.34-26920C>A		intron_variant	Intron 1 of 7	1	NM_001987.5	ENSP00000379658.3
ETV6	ENST00000541426.1	n.218-26920C>A		intron_variant	Intron 1 of 3	4
ETV6	ENST00000544715.1	n.307+8787C>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44010 AN: 151782 Hom.: 6931 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.290 AC: 44020 AN: 151900 Hom.: 6930 Cov.: 31 AF XY: 0.295 AC XY: 21888 AN XY: 74234

African (AFR) AF: 0.160 AC: 6646 AN: 41436

American (AMR) AF: 0.254 AC: 3885 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3464

East Asian (EAS) AF: 0.452 AC: 2327 AN: 5146

South Asian (SAS) AF: 0.384 AC: 1848 AN: 4814

European-Finnish (FIN) AF: 0.363 AC: 3822 AN: 10524

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23368 AN: 67924

Other (OTH) AF: 0.291 AC: 612 AN: 2106

Alfa AF: 0.298 Hom.: 1095

Bravo AF: 0.275

Asia WGS AF: 0.399 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.79
DANN	Benign	0.30
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2900208; hg19: chr12-11878464; COSMIC: COSV67151349;