NM_152594.3:c.-2A>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152594.3(SPRED1):c.-2A>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000696 in 1,579,638 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 Uncertain significance (★★).
Frequency
Consequence
NM_152594.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPRED1 | ENST00000299084 | c.-2A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 7 | 1 | NM_152594.3 | ENSP00000299084.4 | |||
SPRED1 | ENST00000299084 | c.-2A>T | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_152594.3 | ENSP00000299084.4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000101 AC: 2AN: 198896Hom.: 0 AF XY: 0.0000188 AC XY: 2AN XY: 106180
GnomAD4 exome AF: 0.0000743 AC: 106AN: 1427514Hom.: 0 Cov.: 31 AF XY: 0.0000608 AC XY: 43AN XY: 706668
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The c.-2A>T variant is located in the 5' untranslated region (5’ UTR) of the SPRED1 gene. This variant results from an A to T substitution 2 nucleotides upstream from the first translated codon. Based on nucleotide sequence alignment, this position is highly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Noonan syndrome and Noonan-related syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at