chr3-15434411-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_033083.7(EAF1):c.399G>A(p.Thr133=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00359 in 1,614,156 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 85 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 80 hom. )
Consequence
EAF1
NM_033083.7 synonymous
NM_033083.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.49
Genes affected
EAF1 (HGNC:20907): (ELL associated factor 1) Enables transcription elongation regulator activity. Involved in regulation of transcription elongation from RNA polymerase II promoter. Located in intercellular bridge and nuclear body. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 3-15434411-G-A is Benign according to our data. Variant chr3-15434411-G-A is described in ClinVar as [Benign]. Clinvar id is 787010.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.49 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0607 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EAF1 | NM_033083.7 | c.399G>A | p.Thr133= | synonymous_variant | 4/6 | ENST00000396842.7 | |
EAF1 | XM_011534165.2 | c.96G>A | p.Thr32= | synonymous_variant | 3/5 | ||
EAF1 | XM_011534166.2 | c.96G>A | p.Thr32= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EAF1 | ENST00000396842.7 | c.399G>A | p.Thr133= | synonymous_variant | 4/6 | 1 | NM_033083.7 | P1 | |
METTL6 | ENST00000598878.1 | c.-125+4767C>T | intron_variant | 5 | |||||
EAF1 | ENST00000449565.1 | c.*58G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0187 AC: 2842AN: 152148Hom.: 85 Cov.: 32
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GnomAD3 exomes AF: 0.00490 AC: 1231AN: 251402Hom.: 35 AF XY: 0.00354 AC XY: 481AN XY: 135874
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GnomAD4 exome AF: 0.00202 AC: 2946AN: 1461890Hom.: 80 Cov.: 30 AF XY: 0.00168 AC XY: 1221AN XY: 727246
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GnomAD4 genome ? AF: 0.0187 AC: 2843AN: 152266Hom.: 85 Cov.: 32 AF XY: 0.0184 AC XY: 1373AN XY: 74450
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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 submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at