rs1053129
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000791.4(DHFR):c.*2186G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.27 ( 4457 hom., cov: 18)
Exomes 𝑓: 0.19 ( 218 hom. )
Failed GnomAD Quality Control
Consequence
DHFR
NM_000791.4 3_prime_UTR
NM_000791.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.308
Genes affected
DHFR (HGNC:2861): (dihydrofolate reductase) Dihydrofolate reductase converts dihydrofolate into tetrahydrofolate, a methyl group shuttle required for the de novo synthesis of purines, thymidylic acid, and certain amino acids. While the functional dihydrofolate reductase gene has been mapped to chromosome 5, multiple intronless processed pseudogenes or dihydrofolate reductase-like genes have been identified on separate chromosomes. Dihydrofolate reductase deficiency has been linked to megaloblastic anemia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2014]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHFR | NM_000791.4 | c.*2186G>T | 3_prime_UTR_variant | 6/6 | ENST00000439211.7 | ||
DHFR | NM_001290354.2 | c.*2186G>T | 3_prime_UTR_variant | 5/5 | |||
DHFR | NM_001290357.2 | c.*2244G>T | 3_prime_UTR_variant | 5/5 | |||
DHFR | NR_110936.2 | n.3067G>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHFR | ENST00000439211.7 | c.*2186G>T | 3_prime_UTR_variant | 6/6 | 1 | NM_000791.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.271 AC: 33009AN: 121596Hom.: 4454 Cov.: 18
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.186 AC: 3437AN: 18488Hom.: 218 Cov.: 0 AF XY: 0.189 AC XY: 1617AN XY: 8556
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.271 AC: 33018AN: 121636Hom.: 4457 Cov.: 18 AF XY: 0.270 AC XY: 15633AN XY: 57986
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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