rs857716
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003126.4(SPTA1):c.6549-12G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000243 in 1,608,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003126.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTA1 | NM_003126.4 | c.6549-12G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000643759.2 | |||
SPTA1 | XM_011509916.3 | c.6549-12G>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
SPTA1 | XM_011509917.4 | c.6531-12G>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
SPTA1 | XM_047428883.1 | c.6228-12G>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTA1 | ENST00000643759.2 | c.6549-12G>T | splice_polypyrimidine_tract_variant, intron_variant | NM_003126.4 | P1 | ||||
SPTA1 | ENST00000492934.1 | n.64-12G>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
SPTA1 | ENST00000498708.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151948Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000117 AC: 29AN: 248152Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134632
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1456136Hom.: 0 Cov.: 32 AF XY: 0.0000276 AC XY: 20AN XY: 724772
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 152066Hom.: 1 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at