ENST00000643789.1:n.*2610C>T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000643789.1(ENSG00000285269):n.*2610C>T 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 0.0000149 in 1,608,936 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 Uncertain significance (★).
Frequency
Consequence
ENST00000643789.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
- 46,XY disorder of sex development due to 17-beta-hydroxysteroid dehydrogenase 3 deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000285269 | ENST00000643789.1 | n.*2610C>T | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000494818.1 | |||||
HSD17B3 | ENST00000375263.8 | c.*1C>T | 3_prime_UTR_variant | Exon 11 of 11 | 1 | NM_000197.2 | ENSP00000364412.3 | |||
ENSG00000285269 | ENST00000643789.1 | n.*2610C>T | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000494818.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000281 AC: 7AN: 248780 AF XY: 0.0000297 show subpopulations
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1456726Hom.: 0 Cov.: 29 AF XY: 0.0000179 AC XY: 13AN XY: 724760 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356 show subpopulations
ClinVar
Submissions by phenotype
Testosterone 17-beta-dehydrogenase deficiency Uncertain: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 did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at