rs10505762

chr12-11837676-C-T

Variant summary

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

The NM_001987.5(ETV6):c.164-1464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,180 control chromosomes in the GnomAD database, including 2,490 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 0.17 (2490 hom., cov: 32)
• Consequence: ETV6 NM_001987.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETV6	NM_001987.5	c.164-1464C>T		intron_variant		ENST00000396373.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETV6	ENST00000396373.9	c.164-1464C>T		intron_variant		1	NM_001987.5	P1
ETV6	ENST00000545027.1	c.80-1464C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26284 AN: 152062 Hom.: 2489 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.173 AC: 26301 AN: 152180 Hom.: 2490 Cov.: 32 AF XY: 0.174 AC XY: 12923 AN XY: 74404

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.165

Alfa AF: 0.157 Hom.: 2662

Bravo AF: 0.173

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	15
Dann	Benign	0.78

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

Other links and lift over

dbSNP: rs10505762; hg19: chr12-11990610; COSMIC: COSV67147934;