6-36375950-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000340181.9(ETV7):c.228G>A(p.Ala76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,613,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00027 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00025 ( 0 hom. )
Consequence
ETV7
ENST00000340181.9 synonymous
ENST00000340181.9 synonymous
Scores
8
Clinical Significance
Conservation
PhyloP100: -5.18
Genes affected
ETV7 (HGNC:18160): (ETS variant transcription factor 7) The protein encoded by this gene belongs to the ETS family of transcription factors, which is a large group of evolutionarily conserved transcriptional regulators that play an important role in a variety of cellular processes throughout development and differentiation, and are involved in oncogenesis as well. This protein is predominantly expressed in hematopoietic tissues. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene (PMID:11108721).[provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.056855142).
BP6
Variant 6-36375950-C-T is Benign according to our data. Variant chr6-36375950-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2591711.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-5.18 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ETV7 | NM_016135.4 | c.228G>A | p.Ala76= | synonymous_variant | 3/8 | ENST00000340181.9 | NP_057219.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ETV7 | ENST00000340181.9 | c.228G>A | p.Ala76= | synonymous_variant | 3/8 | 1 | NM_016135.4 | ENSP00000341843 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000191 AC: 48AN: 250852Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135640
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GnomAD4 exome AF: 0.000246 AC: 360AN: 1461340Hom.: 0 Cov.: 32 AF XY: 0.000252 AC XY: 183AN XY: 727004
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GnomAD4 genome AF: 0.000269 AC: 41AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
N;N;N;N;N
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at