1-158683388-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_003126.4(SPTA1):c.373G>A(p.Ala125Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,613,308 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003126.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000980 AC: 149AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000742 AC: 185AN: 249190Hom.: 1 AF XY: 0.000755 AC XY: 102AN XY: 135184
GnomAD4 exome AF: 0.00153 AC: 2234AN: 1461102Hom.: 5 Cov.: 31 AF XY: 0.00148 AC XY: 1075AN XY: 726840
GnomAD4 genome AF: 0.000979 AC: 149AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000873 AC XY: 65AN XY: 74426
ClinVar
Submissions by phenotype
not provided Uncertain:3Benign:1
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not specified Uncertain:1
The c.373G>A (p.A125T) alteration is located in exon 3 (coding exon 3) of the SPTA1 gene. This alteration results from a G to A substitution at nucleotide position 373, causing the alanine (A) at amino acid position 125 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
SPTA1-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