6-7593746-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152551.4(SNRNP48):āc.169A>Gā(p.Ile57Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,424,458 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_152551.4 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 |
---|---|---|---|---|---|---|---|
SNRNP48 | NM_152551.4 | c.169A>G | p.Ile57Val | missense_variant | 2/9 | ENST00000342415.6 | |
SNRNP48 | XM_011514312.4 | c.106A>G | p.Ile36Val | missense_variant | 2/9 | ||
SNRNP48 | XM_047418238.1 | c.169A>G | p.Ile57Val | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNRNP48 | ENST00000342415.6 | c.169A>G | p.Ile57Val | missense_variant | 2/9 | 1 | NM_152551.4 | P1 | |
SNRNP48 | ENST00000634363.1 | c.169A>G | p.Ile57Val | missense_variant, NMD_transcript_variant | 2/8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000218 AC: 31AN: 1424458Hom.: 0 Cov.: 29 AF XY: 0.0000170 AC XY: 12AN XY: 706910
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.169A>G (p.I57V) alteration is located in exon 2 (coding exon 2) of the SNRNP48 gene. This alteration results from a A to G substitution at nucleotide position 169, causing the isoleucine (I) at amino acid position 57 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
Publications
No publications associated with this variant yet.