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chr3-186052307-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_004454.3(ETV5):​c.1210-176C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 152,284 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.034 ( 113 hom., cov: 32)

Consequence

ETV5
NM_004454.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.27
Variant links:
Genes affected
ETV5 (HGNC:3494): (ETS variant transcription factor 5) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in cellular response to oxidative stress; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 3-186052307-G-T is Benign according to our data. Variant chr3-186052307-G-T is described in ClinVar as [Benign]. Clinvar id is 1282711.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0344 (5234/152284) while in subpopulation NFE AF= 0.049 (3334/68020). AF 95% confidence interval is 0.0476. There are 113 homozygotes in gnomad4. There are 2586 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 5234 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ETV5NM_004454.3 linkuse as main transcriptc.1210-176C>A intron_variant ENST00000306376.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ETV5ENST00000306376.10 linkuse as main transcriptc.1210-176C>A intron_variant 1 NM_004454.3 P1P41161-1
ETV5ENST00000434744.5 linkuse as main transcriptc.1210-176C>A intron_variant 1 P1P41161-1
ETV5ENST00000433149.1 linkuse as main transcriptc.219-176C>A intron_variant, NMD_transcript_variant 5
ETV5ENST00000480706.1 linkuse as main transcriptn.384-176C>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0344
AC:
5235
AN:
152166
Hom.:
113
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00965
Gnomad AMI
AF:
0.0297
Gnomad AMR
AF:
0.0350
Gnomad ASJ
AF:
0.0173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0103
Gnomad FIN
AF:
0.0708
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0490
Gnomad OTH
AF:
0.0358
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0344
AC:
5234
AN:
152284
Hom.:
113
Cov.:
32
AF XY:
0.0347
AC XY:
2586
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.00962
Gnomad4 AMR
AF:
0.0349
Gnomad4 ASJ
AF:
0.0173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0106
Gnomad4 FIN
AF:
0.0708
Gnomad4 NFE
AF:
0.0490
Gnomad4 OTH
AF:
0.0354
Alfa
AF:
0.0428
Hom.:
28
Bravo
AF:
0.0301
Asia WGS
AF:
0.00664
AC:
26
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
16
DANN
Benign
0.49

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs74607992; hg19: chr3-185770096; API