chr9-128594259-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001130438.3(SPTAN1):c.3300G>A(p.Ala1100Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,614,044 control chromosomes in the GnomAD database, including 218 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001130438.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0209 AC: 3173AN: 152032Hom.: 115 Cov.: 32
GnomAD3 exomes AF: 0.00550 AC: 1382AN: 251452Hom.: 38 AF XY: 0.00407 AC XY: 553AN XY: 135890
GnomAD4 exome AF: 0.00223 AC: 3256AN: 1461894Hom.: 101 Cov.: 32 AF XY: 0.00191 AC XY: 1388AN XY: 727248
GnomAD4 genome AF: 0.0209 AC: 3187AN: 152150Hom.: 117 Cov.: 32 AF XY: 0.0208 AC XY: 1550AN XY: 74372
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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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. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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not provided Benign:1
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Developmental and epileptic encephalopathy, 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at