9-14737462-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001379081.2(FREM1):c.6474G>A(p.Gly2158Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000206 in 1,613,794 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001379081.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FREM1 | NM_001379081.2 | c.6474G>A | p.Gly2158Gly | synonymous_variant | Exon 37 of 37 | ENST00000380880.4 | NP_001366010.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000365 AC: 91AN: 249006Hom.: 1 AF XY: 0.000533 AC XY: 72AN XY: 135104
GnomAD4 exome AF: 0.000213 AC: 311AN: 1461590Hom.: 3 Cov.: 30 AF XY: 0.000301 AC XY: 219AN XY: 727064
GnomAD4 genome AF: 0.000145 AC: 22AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
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FREM1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at