chrX-154438830-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001493.3(GDI1):āc.219T>Cā(p.Asn73Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,203,854 control chromosomes in the GnomAD database, including 16,368 homozygotes. There are 63,336 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_001493.3 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 |
---|---|---|---|---|---|---|---|---|
GDI1 | NM_001493.3 | c.219T>C | p.Asn73Asn | synonymous_variant | Exon 3 of 11 | ENST00000447750.7 | NP_001484.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.275 AC: 30214AN: 109853Hom.: 5001 Cov.: 23 AF XY: 0.264 AC XY: 8538AN XY: 32385
GnomAD3 exomes AF: 0.180 AC: 32984AN: 183494Hom.: 3232 AF XY: 0.170 AC XY: 11558AN XY: 67930
GnomAD4 exome AF: 0.152 AC: 166163AN: 1093942Hom.: 11352 Cov.: 29 AF XY: 0.152 AC XY: 54758AN XY: 359750
GnomAD4 genome AF: 0.275 AC: 30278AN: 109912Hom.: 5016 Cov.: 23 AF XY: 0.264 AC XY: 8578AN XY: 32452
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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. -
Intellectual disability, X-linked 41 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at