rs1241478218
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_152594.3(SPRED1):c.208-6T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_152594.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPRED1 | NM_152594.3 | c.208-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000299084.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPRED1 | ENST00000299084.9 | c.208-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_152594.3 | P1 | |||
SPRED1 | ENST00000561317.1 | c.145-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 4 | |||||
SPRED1 | ENST00000561205.1 | n.546-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250982Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135728
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461354Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726982
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 29, 2021 | The c.208-6T>C intronic alteration consists of a T to C substitution 6 nucleotides before coding exon 3 in the SPRED1 gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Legius syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at