1-109236555-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_006513.4(SARS1):c.1257+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,597,244 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 Benign (★).
Frequency
Consequence
NM_006513.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SARS1 | NM_006513.4 | c.1257+7G>A | splice_region_variant, intron_variant | Intron 9 of 10 | ENST00000234677.7 | NP_006504.2 | ||
SARS1 | NM_001330669.1 | c.1257+7G>A | splice_region_variant, intron_variant | Intron 9 of 11 | NP_001317598.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SARS1 | ENST00000234677.7 | c.1257+7G>A | splice_region_variant, intron_variant | Intron 9 of 10 | 1 | NM_006513.4 | ENSP00000234677.2 | |||
SARS1 | ENST00000369923.4 | c.1257+7G>A | splice_region_variant, intron_variant | Intron 9 of 11 | 5 | ENSP00000358939.4 | ||||
SARS1 | ENST00000468588.1 | n.325G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000605 AC: 92AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 250864Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135632
GnomAD4 exome AF: 0.0000616 AC: 89AN: 1445004Hom.: 0 Cov.: 32 AF XY: 0.0000476 AC XY: 34AN XY: 714672
GnomAD4 genome AF: 0.000604 AC: 92AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at