rs79868029

Variant names:

• chr17-43545139-A-G
• rs79868029
• NM_001079675.5:c.155-117T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-43545139-A-G
• chr17-43545139-A-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001079675.5(ETV4):​c.155-117T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,322,984 control chromosomes in the GnomAD database, including 61,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.26 (5582 hom., cov: 29)
  • Exomes 𝑓: 0.30 (55463 hom.)
• Consequence: ETV4 NM_001079675.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0230
• Publications: 7 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 17-43545139-A-G is Benign according to our data. Variant chr17-43545139-A-G is described in ClinVar as Benign. ClinVar VariationId is 1258836.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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.155-117T>C		intron	N/A	NP_001073143.1	P43268-1
	ETV4	NM_001369366.2		c.155-117T>C		intron	N/A	NP_001356295.1	P43268-1
	ETV4	NM_001986.4		c.155-117T>C		intron	N/A	NP_001977.1	P43268-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETV4	ENST00000319349.10	TSL:1 MANE Select	c.155-117T>C		intron	N/A	ENSP00000321835.4	P43268-1
	ETV4	ENST00000393664.6	TSL:1	c.155-117T>C		intron	N/A	ENSP00000377273.1	P43268-1
	ETV4	ENST00000591713.5	TSL:1	c.155-117T>C		intron	N/A	ENSP00000465718.1	P43268-1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38686 AN: 150880 Hom.: 5582 Cov.: 29

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.301 AC: 352495 AN: 1171984 Hom.: 55463 Cov.: 15 AF XY: 0.301 AC XY: 178317 AN XY: 592330

African (AFR) AF: 0.117 AC: 3232 AN: 27574

American (AMR) AF: 0.240 AC: 9453 AN: 39326

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 6893 AN: 23622

East Asian (EAS) AF: 0.362 AC: 13759 AN: 37988

South Asian (SAS) AF: 0.277 AC: 21885 AN: 79088

European-Finnish (FIN) AF: 0.383 AC: 19928 AN: 51988

Middle Eastern (MID) AF: 0.289 AC: 1348 AN: 4664

European-Non Finnish (NFE) AF: 0.305 AC: 261888 AN: 857292

Other (OTH) AF: 0.280 AC: 14109 AN: 50442

GnomAD4 genome AF: 0.256 AC: 38687 AN: 151000 Hom.: 5582 Cov.: 29 AF XY: 0.259 AC XY: 19099 AN XY: 73658

African (AFR) AF: 0.123 AC: 5048 AN: 41076

American (AMR) AF: 0.229 AC: 3483 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1039 AN: 3456

East Asian (EAS) AF: 0.318 AC: 1618 AN: 5094

South Asian (SAS) AF: 0.276 AC: 1312 AN: 4762

European-Finnish (FIN) AF: 0.389 AC: 4028 AN: 10342

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21271 AN: 67754

Other (OTH) AF: 0.250 AC: 526 AN: 2106

Alfa AF: 0.282 Hom.: 810

Bravo AF: 0.238

Asia WGS AF: 0.222 AC: 771 AN: 3472

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.0
DANN	Benign	0.55
PhyloP100		0.023
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: rs79868029; hg19: chr17-41622507; COSMIC: COSV60044187; COSMIC: COSV60044187;