chr9-124890381-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002077.4(GOLGA1):c.1497+8C>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 0.000206 in 1,595,610 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 Benign (★).
Frequency
Consequence
NM_002077.4 splice_region, 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 |
---|---|---|---|---|---|---|---|
GOLGA1 | NM_002077.4 | c.1497+8C>G | splice_region_variant, intron_variant | ENST00000373555.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA1 | ENST00000373555.9 | c.1497+8C>G | splice_region_variant, intron_variant | 1 | NM_002077.4 | P1 | |||
GOLGA1 | ENST00000475407.5 | c.*643+8C>G | splice_region_variant, intron_variant, NMD_transcript_variant | 5 | |||||
GOLGA1 | ENST00000485337.1 | c.*251+8C>G | splice_region_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00108 AC: 165AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000274 AC: 69AN: 251390Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135876
GnomAD4 exome AF: 0.000112 AC: 162AN: 1443342Hom.: 0 Cov.: 29 AF XY: 0.000103 AC XY: 74AN XY: 719428
GnomAD4 genome ? AF: 0.00110 AC: 167AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.00101 AC XY: 75AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 24, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at