2-45413118-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018079.5(SRBD1):āc.2509A>Gā(p.Met837Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,613,518 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018079.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRBD1 | NM_018079.5 | c.2509A>G | p.Met837Val | missense_variant | 19/21 | ENST00000263736.5 | NP_060549.4 | |
SRBD1 | XM_011532946.3 | c.2461A>G | p.Met821Val | missense_variant | 19/21 | XP_011531248.1 | ||
SRBD1 | XM_047444861.1 | c.1066A>G | p.Met356Val | missense_variant | 11/13 | XP_047300817.1 | ||
SRBD1 | XM_047444862.1 | c.1066A>G | p.Met356Val | missense_variant | 10/12 | XP_047300818.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRBD1 | ENST00000263736.5 | c.2509A>G | p.Met837Val | missense_variant | 19/21 | 2 | NM_018079.5 | ENSP00000263736 | P1 | |
SRBD1 | ENST00000490133.5 | n.1406A>G | non_coding_transcript_exon_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250672Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135428
GnomAD4 exome AF: 0.000145 AC: 212AN: 1461198Hom.: 0 Cov.: 30 AF XY: 0.000150 AC XY: 109AN XY: 726850
GnomAD4 genome AF: 0.000158 AC: 24AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.2509A>G (p.M837V) alteration is located in exon 19 (coding exon 18) of the SRBD1 gene. This alteration results from a A to G substitution at nucleotide position 2509, causing the methionine (M) at amino acid position 837 to be replaced by a valine (V). 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