rs2298839
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001134.3(AFP):c.843+5A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,612,764 control chromosomes in the GnomAD database, including 253,780 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Benign (no stars).
Frequency
Consequence
NM_001134.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AFP | NM_001134.3 | c.843+5A>G | splice_region_variant, intron_variant | ENST00000395792.7 | NP_001125.1 | |||
AFP | NM_001354717.2 | c.369+5A>G | splice_region_variant, intron_variant | NP_001341646.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AFP | ENST00000395792.7 | c.843+5A>G | splice_region_variant, intron_variant | 1 | NM_001134.3 | ENSP00000379138.2 | ||||
AFP | ENST00000226359.2 | c.843+5A>G | splice_region_variant, intron_variant | 5 | ENSP00000226359.2 |
Frequencies
GnomAD3 genomes AF: 0.520 AC: 78965AN: 151818Hom.: 20984 Cov.: 31
GnomAD3 exomes AF: 0.541 AC: 135915AN: 251370Hom.: 37490 AF XY: 0.544 AC XY: 73900AN XY: 135870
GnomAD4 exome AF: 0.562 AC: 821274AN: 1460826Hom.: 232802 Cov.: 43 AF XY: 0.562 AC XY: 408108AN XY: 726726
GnomAD4 genome AF: 0.520 AC: 78973AN: 151938Hom.: 20978 Cov.: 31 AF XY: 0.517 AC XY: 38397AN XY: 74260
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at