5-31515550-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001382508.1(DROSHA):c.962C>T(p.Ser321Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 1,548,624 control chromosomes in the GnomAD database, including 172,082 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001382508.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DROSHA | NM_001382508.1 | c.962C>T | p.Ser321Leu | missense_variant | 7/36 | ENST00000344624.8 | |
DROSHA | NM_013235.5 | c.962C>T | p.Ser321Leu | missense_variant | 6/35 | ||
DROSHA | NM_001100412.2 | c.948-331C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DROSHA | ENST00000344624.8 | c.962C>T | p.Ser321Leu | missense_variant | 7/36 | 5 | NM_001382508.1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.362 AC: 54972AN: 151998Hom.: 12286 Cov.: 33
GnomAD3 exomes AF: 0.432 AC: 66716AN: 154384Hom.: 15445 AF XY: 0.439 AC XY: 35897AN XY: 81730
GnomAD4 exome AF: 0.470 AC: 657025AN: 1396508Hom.: 159797 Cov.: 34 AF XY: 0.471 AC XY: 324779AN XY: 688940
GnomAD4 genome AF: 0.361 AC: 54975AN: 152116Hom.: 12285 Cov.: 33 AF XY: 0.363 AC XY: 27009AN XY: 74346
ClinVar
Submissions by phenotype
DROSHA-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at