NM_020975.6:c.-37G>C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_020975.6(RET):c.-37G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000115 in 1,474,730 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020975.6 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RET | NM_020975.6 | c.-37G>C | 5_prime_UTR_variant | Exon 1 of 20 | ENST00000355710.8 | NP_066124.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151978Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000339 AC: 3AN: 88482Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 49940
GnomAD4 exome AF: 0.00000832 AC: 11AN: 1322752Hom.: 0 Cov.: 30 AF XY: 0.00000307 AC XY: 2AN XY: 650982
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151978Hom.: 0 Cov.: 35 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
Multiple endocrine neoplasia type 2A;C0025269:Multiple endocrine neoplasia type 2B;C0031511:Pheochromocytoma;C1833921:Familial medullary thyroid carcinoma;C3888239:Hirschsprung disease, susceptibility to, 1 Uncertain:1
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Multiple endocrine neoplasia, type 2 Uncertain:1
This variant occurs in a non-coding region of the RET gene. It does not change the encoded amino acid sequence of the RET protein. This variant is present in population databases (rs751005619, gnomAD 0.07%). This variant has been observed in individual(s) with Hirschsprung disease (PMID: 14633923). ClinVar contains an entry for this variant (Variation ID: 477374). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
not provided Benign:1
See Variant Classification Assertion Criteria. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at