22-26490160-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001013694.3(SRRD):c.726G>A(p.Met242Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013694.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRRD | NM_001013694.3 | c.726G>A | p.Met242Ile | missense_variant | 5/7 | ENST00000215917.11 | |
SRRD | XM_011530178.3 | c.513G>A | p.Met171Ile | missense_variant | 5/7 | ||
SRRD | XM_017028799.3 | c.610-865G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRRD | ENST00000215917.11 | c.726G>A | p.Met242Ile | missense_variant | 5/7 | 1 | NM_001013694.3 | P1 | |
SRRD | ENST00000477945.1 | n.523G>A | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249546Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135396
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727236
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2021 | The c.726G>A (p.M242I) alteration is located in exon 5 (coding exon 5) of the SRRD gene. This alteration results from a G to A substitution at nucleotide position 726, causing the methionine (M) at amino acid position 242 to be replaced by an isoleucine (I). 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