7-73700757-G-A
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 1P and 6B. PP2BP4_StrongBP6_Moderate
The ENST00000395156.7(STX1A):c.716C>T(p.Pro239Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000395156.7 missense
Scores
Clinical Significance
Conservation
Publications
- complex neurodevelopmental disorderInheritance: AD Classification: MODERATE Submitted by: G2P
- cystic fibrosisInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- neurodevelopmental disorderInheritance: AR Classification: LIMITED Submitted by: G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STX1A | NM_004603.4 | c.762C>T | p.Ala254Ala | synonymous_variant | Exon 9 of 10 | ENST00000222812.8 | NP_004594.1 | |
STX1A | NM_001165903.2 | c.716C>T | p.Pro239Leu | missense_variant | Exon 9 of 10 | NP_001159375.1 | ||
STX1A | XM_047420777.1 | c.*125C>T | 3_prime_UTR_variant | Exon 9 of 9 | XP_047276733.1 | |||
STX1A | XM_047420778.1 | c.*70C>T | 3_prime_UTR_variant | Exon 9 of 9 | XP_047276734.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151992Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251348 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461712Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727178 show subpopulations
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151992Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74228 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely 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