chr6-111310106-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001372078.1(REV3L):c.8796-7C>T 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 0.000267 in 1,488,816 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REV3L | NM_001372078.1 | c.8796-7C>T | 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.8796-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001372078.1 | P4 | |||
ENST00000607434.1 | n.904G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 151768Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 26AN: 171274Hom.: 0 AF XY: 0.000130 AC XY: 12AN XY: 92032
GnomAD4 exome AF: 0.000280 AC: 374AN: 1337048Hom.: 0 Cov.: 30 AF XY: 0.000291 AC XY: 191AN XY: 656046
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 151768Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74068
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at