chr12-11659396-A-G

Position:

• chr12-11659396-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001987.5(ETV6):​c.33+9236A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,016 control chromosomes in the GnomAD database, including 13,006 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 (13006 hom., cov: 31)
• Consequence: ETV6 NM_001987.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETV6	NM_001987.5	c.33+9236A>G		intron_variant		ENST00000396373.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETV6	ENST00000396373.9	c.33+9236A>G		intron_variant		1	NM_001987.5	P1
ETV6	ENST00000541426.1	n.217+9236A>G		intron_variant, non_coding_transcript_variant		4
ETV6	ENST00000544715.1	n.150+9236A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56866 AN: 151898 Hom.: 13002 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.374 AC: 56873 AN: 152016 Hom.: 13006 Cov.: 31 AF XY: 0.375 AC XY: 27867 AN XY: 74288

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.402

Alfa AF: 0.480 Hom.: 30842

Bravo AF: 0.360

Asia WGS AF: 0.327 AC: 1132 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	6.7
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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

Other links and lift over

dbSNP: rs916041; hg19: chr12-11812330;