chr6-111310105-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001372078.1(REV3L):c.8796-6G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,490,546 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001372078.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REV3L | NM_001372078.1 | c.8796-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000368802.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REV3L | ENST00000368802.8 | c.8796-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001372078.1 | P4 | |||
ENST00000607434.1 | n.903C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00268 AC: 407AN: 151914Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00399 AC: 695AN: 174238Hom.: 14 AF XY: 0.00319 AC XY: 299AN XY: 93850
GnomAD4 exome AF: 0.000840 AC: 1125AN: 1338514Hom.: 22 Cov.: 30 AF XY: 0.000758 AC XY: 498AN XY: 657252
GnomAD4 genome ? AF: 0.00268 AC: 408AN: 152032Hom.: 3 Cov.: 32 AF XY: 0.00280 AC XY: 208AN XY: 74312
ClinVar
Submissions by phenotype
REV3L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 05, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at