17-43530602-ACGCG-ACG

Variant names:

• chr17-43530602-ACG-A
• rs200376976
• NM_001079675.5:c.812-423_812-422delCG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001079675.5(ETV4):​c.812-423_812-422delCG 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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079675.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETV4	NM_001079675.5	MANE Select	c.812-423_812-422delCG		intron	N/A	NP_001073143.1	P43268-1
	DHX8	NM_001322219.2		c.3444-5803_3444-5802delCG		intron	N/A	NP_001309148.1	K7END7
	ETV4	NM_001369366.2		c.812-423_812-422delCG		intron	N/A	NP_001356295.1	P43268-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETV4	ENST00000319349.10	TSL:1 MANE Select	c.812-423_812-422delCG		intron	N/A	ENSP00000321835.4	P43268-1
	ETV4	ENST00000393664.6	TSL:1	c.812-423_812-422delCG		intron	N/A	ENSP00000377273.1	P43268-1
	ETV4	ENST00000591713.5	TSL:1	c.812-423_812-422delCG		intron	N/A	ENSP00000465718.1	P43268-1

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

African (AFR) AF: 0.381 AC: 13073 AN: 34350

American (AMR) AF: 0.427 AC: 5912 AN: 13850

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1278 AN: 3012

East Asian (EAS) AF: 0.438 AC: 1914 AN: 4374

South Asian (SAS) AF: 0.338 AC: 1379 AN: 4082

European-Finnish (FIN) AF: 0.364 AC: 3223 AN: 8850

Middle Eastern (MID) AF: 0.337 AC: 83 AN: 246

European-Non Finnish (NFE) AF: 0.407 AC: 24949 AN: 61290

Other (OTH) AF: 0.424 AC: 788 AN: 1858

Alfa AF: 0.150 Hom.: 231

Asia WGS AF: 0.357 AC: 1229 AN: 3442

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.66
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: rs200376976; hg19: chr17-41607970; COSMIC: COSV52251706; COSMIC: COSV52251706;