7-83961370-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_006080.3(SEMA3A):c.*1G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006080.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.*1G>A | 3_prime_UTR_variant | Exon 17 of 17 | ENST00000265362.9 | NP_006071.1 | ||
SEMA3A | XM_005250110.4 | c.*1G>A | 3_prime_UTR_variant | Exon 20 of 20 | XP_005250167.1 | |||
SEMA3A | XM_047419751.1 | c.*1G>A | 3_prime_UTR_variant | Exon 21 of 21 | XP_047275707.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251216Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135774
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460822Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 726800
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74336
ClinVar
Submissions by phenotype
SEMA3A-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