19-43612351-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001145641.2(SRRM5):c.230G>A(p.Arg77Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000722 in 1,551,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001145641.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRRM5 | NM_001145641.2 | c.230G>A | p.Arg77Gln | missense_variant | 1/1 | ENST00000417606.3 | |
ZNF428 | NM_182498.4 | c.76+1878C>T | intron_variant | ENST00000300811.8 | |||
ZNF428 | XM_047438168.1 | c.76+1878C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRRM5 | ENST00000417606.3 | c.230G>A | p.Arg77Gln | missense_variant | 1/1 | NM_001145641.2 | P1 | ||
ZNF428 | ENST00000300811.8 | c.76+1878C>T | intron_variant | 1 | NM_182498.4 | P1 | |||
SRRM5 | ENST00000607544.1 | c.230G>A | p.Arg77Gln | missense_variant | 3/3 | 2 | P1 | ||
ZNF428 | ENST00000598676.1 | c.76+1878C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000162 AC: 25AN: 154112Hom.: 0 AF XY: 0.000135 AC XY: 11AN XY: 81766
GnomAD4 exome AF: 0.0000686 AC: 96AN: 1399412Hom.: 0 Cov.: 30 AF XY: 0.0000710 AC XY: 49AN XY: 690216
GnomAD4 genome AF: 0.000105 AC: 16AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74310
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at