rs1126744
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004463.3(FGD1):āc.2136A>Gā(p.Pro712Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 1,190,574 control chromosomes in the GnomAD database, including 4,535 homozygotes. There are 16,461 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_004463.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGD1 | NM_004463.3 | c.2136A>G | p.Pro712Pro | synonymous_variant | Exon 14 of 18 | ENST00000375135.4 | NP_004454.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.140 AC: 15410AN: 109762Hom.: 2125 Cov.: 21 AF XY: 0.130 AC XY: 4170AN XY: 32064
GnomAD3 exomes AF: 0.0670 AC: 11999AN: 179080Hom.: 1148 AF XY: 0.0587 AC XY: 3746AN XY: 63864
GnomAD4 exome AF: 0.0358 AC: 38667AN: 1080756Hom.: 2408 Cov.: 28 AF XY: 0.0352 AC XY: 12276AN XY: 348276
GnomAD4 genome AF: 0.141 AC: 15431AN: 109818Hom.: 2127 Cov.: 21 AF XY: 0.130 AC XY: 4185AN XY: 32130
ClinVar
Submissions by phenotype
not specified Benign:3
p.Pro712Pro in exon 14 of FGD1: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 44.23% (3737/8449) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs1126744). -
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not provided Benign:3
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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