11-126267605-AGCACTT-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_003139.4(SRPRA):c.303_308delAAGTGC(p.Gln101_Ala103delinsHis) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000372 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003139.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPRA | NM_003139.4 | c.303_308delAAGTGC | p.Gln101_Ala103delinsHis | disruptive_inframe_deletion | Exon 3 of 14 | ENST00000332118.11 | NP_003130.2 | |
SRPRA | NM_001177842.2 | c.219_224delAAGTGC | p.Gln73_Ala75delinsHis | disruptive_inframe_deletion | Exon 2 of 13 | NP_001171313.1 | ||
SRPRA | XM_047427497.1 | c.303_308delAAGTGC | p.Gln101_Ala103delinsHis | disruptive_inframe_deletion | Exon 3 of 14 | XP_047283453.1 | ||
SRPRA | XM_017018179.3 | c.303_308delAAGTGC | p.Gln101_Ala103delinsHis | disruptive_inframe_deletion | Exon 3 of 14 | XP_016873668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPRA | ENST00000332118.11 | c.303_308delAAGTGC | p.Gln101_Ala103delinsHis | disruptive_inframe_deletion | Exon 3 of 14 | 1 | NM_003139.4 | ENSP00000328023.5 | ||
SRPRA | ENST00000532259.1 | c.219_224delAAGTGC | p.Gln73_Ala75delinsHis | disruptive_inframe_deletion | Exon 2 of 13 | 2 | ENSP00000435508.1 | |||
SRPRA | ENST00000528744.5 | n.419_424delAAGTGC | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
SRPRA | ENST00000530680.1 | n.525_530delAAGTGC | non_coding_transcript_exon_variant | Exon 4 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461810Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727194
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74382
ClinVar
Submissions by phenotype
SRPRA-related disorder Uncertain:1
The SRPRA c.303_308del6 variant is predicted to result in an in-frame deletion (p.Gln101_Ala103delinsHis). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at