NM_020975.6:c.*1969T>C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_020975.6(RET):c.*1969T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 388,468 control chromosomes in the GnomAD database, including 563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_020975.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RET | NM_020975.6 | c.*1969T>C | 3_prime_UTR_variant | Exon 20 of 20 | ENST00000355710.8 | NP_066124.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RET | ENST00000355710.8 | c.*1969T>C | 3_prime_UTR_variant | Exon 20 of 20 | 5 | NM_020975.6 | ENSP00000347942.3 | |||
RET | ENST00000615310.5 | c.*3484T>C | 3_prime_UTR_variant | Exon 17 of 17 | 5 | ENSP00000480088.2 | ||||
RET | ENST00000683007.1 | n.6277T>C | non_coding_transcript_exon_variant | Exon 16 of 16 |
Frequencies
GnomAD3 genomes AF: 0.0438 AC: 6661AN: 152232Hom.: 183 Cov.: 33
GnomAD4 exome AF: 0.0498 AC: 11760AN: 236118Hom.: 380 Cov.: 0 AF XY: 0.0505 AC XY: 6037AN XY: 119564
GnomAD4 genome AF: 0.0438 AC: 6670AN: 152350Hom.: 183 Cov.: 33 AF XY: 0.0437 AC XY: 3259AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is associated with the following publications: (PMID: 16986122) -
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Hirschsprung disease, protection against Benign:1
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Pheochromocytoma Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Renal hypodysplasia/aplasia 1 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Hirschsprung disease, susceptibility to, 1 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Multiple endocrine neoplasia type 2A Benign:1
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Multiple endocrine neoplasia Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at