17-43530602-ACG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001079675.5(ETV4):c.812-423_812-422del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.40 (9287 hom., cov: 0)
• Consequence: ETV4 NM_001079675.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.660

Genes affected

ETV4 (HGNC:3493): (ETS variant transcription factor 4) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of keratinocyte differentiation and positive regulation of transcription by RNA polymerase II. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

DHX8 (HGNC:2749): (DEAH-box helicase 8) This gene is a member of the DEAH box polypeptide family. The encoded protein contains the DEAH (Asp-Glu-Ala-His) motif which is characteristic of all DEAH box proteins, and is thought to function as an ATP-dependent RNA helicase that regulates the release of spliced mRNAs from spliceosomes prior to their export from the nucleus. This protein may be required for the replication of human immunodeficiency virus type 1 (HIV-1). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-43530602-ACG-A is Benign according to our data. Variant chr17-43530602-ACG-A is described in ClinVar as [Benign]. Clinvar id is 1260653.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETV4	NM_001079675.5	c.812-423_812-422del		intron_variant		ENST00000319349.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETV4	ENST00000319349.10	c.812-423_812-422del		intron_variant		1	NM_001079675.5	P1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 52931 AN: 132692 Hom.: 9288 Cov.: 0

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.399 AC: 52937 AN: 132752 Hom.: 9287 Cov.: 0 AF XY: 0.398 AC XY: 25668 AN XY: 64448

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.424

Asia WGS AF: 0.357 AC: 1229 AN: 3442

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs200376976; hg19: chr17-41607970;