rs7387
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000791.4(DHFR):c.*115A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 585,468 control chromosomes in the GnomAD database, including 19,691 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 0.25 ( 5120 hom., cov: 30)
Exomes 𝑓: 0.25 ( 14571 hom. )
Consequence
DHFR
NM_000791.4 3_prime_UTR
NM_000791.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.254
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHFR | NM_000791.4 | c.*115A>T | 3_prime_UTR_variant | 6/6 | ENST00000439211.7 | ||
DHFR | NM_001290354.2 | c.*115A>T | 3_prime_UTR_variant | 5/5 | |||
DHFR | NM_001290357.2 | c.*173A>T | 3_prime_UTR_variant | 5/5 | |||
DHFR | NR_110936.2 | n.996A>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHFR | ENST00000439211.7 | c.*115A>T | 3_prime_UTR_variant | 6/6 | 1 | NM_000791.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38560AN: 151784Hom.: 5114 Cov.: 30
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GnomAD4 exome AF: 0.246 AC: 106652AN: 433566Hom.: 14571 Cov.: 5 AF XY: 0.251 AC XY: 57407AN XY: 229116
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GnomAD4 genome ? AF: 0.254 AC: 38587AN: 151902Hom.: 5120 Cov.: 30 AF XY: 0.251 AC XY: 18636AN XY: 74256
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ClinVar
Not reported inComputational scores
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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