19-6182745-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_030924.5(ACSBG2):c.907-6A>C 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 0.00175 in 1,613,648 control chromosomes in the GnomAD database, including 45 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_030924.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSBG2 | NM_030924.5 | c.907-6A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000588485.6 | |||
LOC105372255 | XR_936282.3 | n.50-6302T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSBG2 | ENST00000588485.6 | c.907-6A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_030924.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00906 AC: 1379AN: 152164Hom.: 26 Cov.: 31
GnomAD3 exomes AF: 0.00245 AC: 614AN: 250746Hom.: 14 AF XY: 0.00191 AC XY: 259AN XY: 135536
GnomAD4 exome AF: 0.000979 AC: 1431AN: 1461366Hom.: 19 Cov.: 32 AF XY: 0.000869 AC XY: 632AN XY: 726984
GnomAD4 genome AF: 0.00913 AC: 1391AN: 152282Hom.: 26 Cov.: 31 AF XY: 0.00855 AC XY: 637AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 08, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at