chr7-82590109-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000320415.6(MTHFD2P5):n.583G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 548,800 control chromosomes in the GnomAD database, including 227,011 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 0.92 ( 65053 hom., cov: 32)
Exomes 𝑓: 0.90 ( 161958 hom. )
Consequence
MTHFD2P5
ENST00000320415.6 non_coding_transcript_exon
ENST00000320415.6 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.64
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFD2P5 | ENST00000320415.6 | n.583G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.924 AC: 140505AN: 152122Hom.: 65010 Cov.: 32
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GnomAD4 exome AF: 0.903 AC: 358259AN: 396560Hom.: 161958 Cov.: 2 AF XY: 0.904 AC XY: 201901AN XY: 223422
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GnomAD4 genome ? AF: 0.924 AC: 140602AN: 152240Hom.: 65053 Cov.: 32 AF XY: 0.922 AC XY: 68612AN XY: 74440
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at