22-26488486-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001013694.3(SRRD):c.607G>A(p.Glu203Lys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,611,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013694.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRRD | NM_001013694.3 | c.607G>A | p.Glu203Lys | missense_variant, splice_region_variant | 4/7 | ENST00000215917.11 | |
SRRD | XM_011530178.3 | c.394G>A | p.Glu132Lys | missense_variant, splice_region_variant | 4/7 | ||
SRRD | XM_017028799.3 | c.607G>A | p.Glu203Lys | missense_variant, splice_region_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRRD | ENST00000215917.11 | c.607G>A | p.Glu203Lys | missense_variant, splice_region_variant | 4/7 | 1 | NM_001013694.3 | P1 | |
SRRD | ENST00000477945.1 | n.404G>A | splice_region_variant, non_coding_transcript_exon_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249402Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135312
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1458934Hom.: 0 Cov.: 32 AF XY: 0.0000441 AC XY: 32AN XY: 725968
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.607G>A (p.E203K) alteration is located in exon 4 (coding exon 4) of the SRRD gene. This alteration results from a G to A substitution at nucleotide position 607, causing the glutamic acid (E) at amino acid position 203 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at