11-126267540-GTC-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_003139.4(SRPRA):c.365+7_365+8delGA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,613,772 control chromosomes in the GnomAD database, including 3 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003139.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPRA | NM_003139.4 | c.365+7_365+8delGA | splice_region_variant, intron_variant | Intron 3 of 13 | ENST00000332118.11 | NP_003130.2 | ||
SRPRA | NM_001177842.2 | c.281+7_281+8delGA | splice_region_variant, intron_variant | Intron 2 of 12 | NP_001171313.1 | |||
SRPRA | XM_047427497.1 | c.365+7_365+8delGA | splice_region_variant, intron_variant | Intron 3 of 13 | XP_047283453.1 | |||
SRPRA | XM_017018179.3 | c.365+7_365+8delGA | splice_region_variant, intron_variant | Intron 3 of 13 | XP_016873668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPRA | ENST00000332118.11 | c.365+7_365+8delGA | splice_region_variant, intron_variant | Intron 3 of 13 | 1 | NM_003139.4 | ENSP00000328023.5 | |||
SRPRA | ENST00000532259.1 | c.281+7_281+8delGA | splice_region_variant, intron_variant | Intron 2 of 12 | 2 | ENSP00000435508.1 | ||||
SRPRA | ENST00000528744.5 | n.488_489delGA | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
SRPRA | ENST00000530680.1 | n.*36_*37delGA | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000171 AC: 43AN: 250842Hom.: 3 AF XY: 0.000155 AC XY: 21AN XY: 135640
GnomAD4 exome AF: 0.000155 AC: 226AN: 1461462Hom.: 3 AF XY: 0.000186 AC XY: 135AN XY: 726996
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74476
ClinVar
Submissions by phenotype
SRPRA-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