rs147035080
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004463.3(FGD1):c.-4G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 1,004,033 control chromosomes in the GnomAD database, including 2,344 homozygotes. There are 25,995 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004463.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGD1 | NM_004463.3 | c.-4G>C | 5_prime_UTR_variant | Exon 1 of 18 | ENST00000375135.4 | NP_004454.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0504 AC: 5563AN: 110276Hom.: 173 Cov.: 22 AF XY: 0.0473 AC XY: 1556AN XY: 32870
GnomAD3 exomes AF: 0.254 AC: 1525AN: 5995Hom.: 43 AF XY: 0.534 AC XY: 383AN XY: 717
GnomAD4 exome AF: 0.0851 AC: 76073AN: 893715Hom.: 2172 Cov.: 29 AF XY: 0.0896 AC XY: 24445AN XY: 272959
GnomAD4 genome AF: 0.0503 AC: 5553AN: 110318Hom.: 172 Cov.: 22 AF XY: 0.0471 AC XY: 1550AN XY: 32922
ClinVar
Submissions by phenotype
not specified Benign:3
c.-4G>C in the 5'UTR of FGD1: This variant is is not expected to have clinical significance because it has been identified in 9.8% (2533/25820) of total chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs147035080). ACMG/AMP Criteria applied: BA1 -
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not provided Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at