chr19-43612519-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145641.2(SRRM5):āc.398A>Gā(p.Lys133Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,551,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001145641.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRRM5 | NM_001145641.2 | c.398A>G | p.Lys133Arg | missense_variant | 1/1 | ENST00000417606.3 | |
ZNF428 | NM_182498.4 | c.76+1710T>C | intron_variant | ENST00000300811.8 | |||
ZNF428 | XM_047438168.1 | c.76+1710T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRRM5 | ENST00000417606.3 | c.398A>G | p.Lys133Arg | missense_variant | 1/1 | NM_001145641.2 | P1 | ||
ZNF428 | ENST00000300811.8 | c.76+1710T>C | intron_variant | 1 | NM_182498.4 | P1 | |||
SRRM5 | ENST00000607544.1 | c.398A>G | p.Lys133Arg | missense_variant | 3/3 | 2 | P1 | ||
ZNF428 | ENST00000598676.1 | c.76+1710T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 154010Hom.: 0 AF XY: 0.0000245 AC XY: 2AN XY: 81720
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1399234Hom.: 0 Cov.: 30 AF XY: 0.00000724 AC XY: 5AN XY: 690136
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.398A>G (p.K133R) alteration is located in exon 1 (coding exon 1) of the SRRM5 gene. This alteration results from a A to G substitution at nucleotide position 398, causing the lysine (K) at amino acid position 133 to be replaced by an arginine (R). 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