ENST00000586764.1:c.-169+4775C>T

Variant names:

• chr17-43574517-G-A
• rs11650719
• ENST00000586764.1:c.-169+4775C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586764.1(ETV4):​c.-169+4775C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,154 control chromosomes in the GnomAD database, including 1,977 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 0.15 (1977 hom., cov: 32)
• Consequence: ETV4 ENST00000586764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586764.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETV4	ENST00000586764.1	TSL:3	c.-169+4775C>T		intron	N/A	ENSP00000466673.1
	DHX8	ENST00000588996.1	TSL:4	n.32-15571G>A		intron	N/A
	DHX8	ENST00000650571.1		n.*426-15571G>A		intron	N/A	ENSP00000496923.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23092 AN: 152036 Hom.: 1976 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.152 AC: 23110 AN: 152154 Hom.: 1977 Cov.: 32 AF XY: 0.148 AC XY: 11015 AN XY: 74388

African (AFR) AF: 0.208 AC: 8633 AN: 41490

American (AMR) AF: 0.0926 AC: 1415 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3468

East Asian (EAS) AF: 0.00926 AC: 48 AN: 5186

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10588

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10186 AN: 68008

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.145 Hom.: 3344

Bravo AF: 0.149

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.88
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs11650719; hg19: chr17-41651885;