9-86046571-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_016548.4(GOLM1):c.366C>T(p.Asp122=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000743 in 1,596,644 control chromosomes in the GnomAD database, including 9 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_016548.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLM1 | NM_016548.4 | c.366C>T | p.Asp122= | splice_region_variant, synonymous_variant | 5/10 | ENST00000388712.7 | |
GOLM1 | NM_177937.3 | c.366C>T | p.Asp122= | splice_region_variant, synonymous_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLM1 | ENST00000388712.7 | c.366C>T | p.Asp122= | splice_region_variant, synonymous_variant | 5/10 | 1 | NM_016548.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00398 AC: 605AN: 152110Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 273AN: 242794Hom.: 2 AF XY: 0.000717 AC XY: 94AN XY: 131114
GnomAD4 exome AF: 0.000402 AC: 581AN: 1444416Hom.: 4 Cov.: 27 AF XY: 0.000334 AC XY: 240AN XY: 719116
GnomAD4 genome AF: 0.00397 AC: 605AN: 152228Hom.: 5 Cov.: 32 AF XY: 0.00356 AC XY: 265AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at