chr13-113105910-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_019616.4(F7):c.64+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000221 in 1,581,512 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_019616.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F7 | NM_019616.4 | c.64+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000346342.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F7 | ENST00000346342.8 | c.64+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_019616.4 | P2 | |||
F7 | ENST00000375581.3 | c.64+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | A2 | ||||
F7 | ENST00000541084.5 | c.64+5G>A | splice_donor_5th_base_variant, intron_variant | 2 | |||||
F7 | ENST00000444337.1 | c.64+5G>A | splice_donor_5th_base_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 151930Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000247 AC: 5AN: 202406Hom.: 0 AF XY: 0.0000185 AC XY: 2AN XY: 108186
GnomAD4 exome AF: 0.0000175 AC: 25AN: 1429582Hom.: 0 Cov.: 31 AF XY: 0.0000156 AC XY: 11AN XY: 707278
GnomAD4 genome AF: 0.0000658 AC: 10AN: 151930Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74176
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at