chr17-39201209-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000981.4(RPL19):c.6-4C>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 0.00000069 in 1,448,372 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_000981.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL19 | NM_000981.4 | c.6-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000225430.9 | |||
LOC124903996 | XR_007065745.1 | n.6G>A | non_coding_transcript_exon_variant | 1/2 | |||
RPL19 | NM_001330200.1 | c.-1-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL19 | ENST00000225430.9 | c.6-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000981.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247224Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134164
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448372Hom.: 0 Cov.: 28 AF XY: 0.00000139 AC XY: 1AN XY: 721290
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at