17-43530609-CGTGTGTGT-C

Variant summary

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

The NM_001079675.5(ETV4):c.812-436_812-429del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (3766 hom., cov: 15)
• Consequence: ETV4 NM_001079675.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.04

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 17-43530609-CGTGTGTGT-C is Benign according to our data. Variant chr17-43530609-CGTGTGTGT-C is described in ClinVar as [Benign]. Clinvar id is 1295940.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETV4	NM_001079675.5	c.812-436_812-429del		intron_variant		ENST00000319349.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETV4	ENST00000319349.10	c.812-436_812-429del		intron_variant		1	NM_001079675.5	P1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 31912 AN: 118948 Hom.: 3766 Cov.: 15

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.268 AC: 31913 AN: 119022 Hom.: 3766 Cov.: 15 AF XY: 0.271 AC XY: 15797 AN XY: 58360

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.286

Bravo AF: 0.202

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 18, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs58803566; hg19: chr17-41607977;