chr14-20891900-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002935.3(RNASE3):c.214C>T(p.Arg72Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00609 in 1,612,940 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002935.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNASE3 | NM_002935.3 | c.214C>T | p.Arg72Cys | missense_variant | 2/2 | ENST00000304639.4 | |
LOC100507513 | XR_110261.4 | n.723-16157G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNASE3 | ENST00000304639.4 | c.214C>T | p.Arg72Cys | missense_variant | 2/2 | 1 | NM_002935.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00434 AC: 657AN: 151212Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00433 AC: 1089AN: 251340Hom.: 7 AF XY: 0.00428 AC XY: 582AN XY: 135870
GnomAD4 exome AF: 0.00627 AC: 9161AN: 1461610Hom.: 50 Cov.: 46 AF XY: 0.00612 AC XY: 4453AN XY: 727154
GnomAD4 genome ? AF: 0.00434 AC: 657AN: 151330Hom.: 4 Cov.: 32 AF XY: 0.00430 AC XY: 318AN XY: 73978
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | RNASE3: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at