2-46758656-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000394861.3(SOCS5):āc.126G>Cā(p.Glu42Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000174 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000394861.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SOCS5 | NM_144949.3 | c.126G>C | p.Glu42Asp | missense_variant | 2/2 | ENST00000394861.3 | NP_659198.1 | |
SOCS5 | NM_014011.5 | c.126G>C | p.Glu42Asp | missense_variant | 2/2 | NP_054730.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOCS5 | ENST00000394861.3 | c.126G>C | p.Glu42Asp | missense_variant | 2/2 | 1 | NM_144949.3 | ENSP00000378330 | P1 | |
SOCS5 | ENST00000306503.5 | c.126G>C | p.Glu42Asp | missense_variant | 2/2 | 1 | ENSP00000305133 | P1 | ||
LINC01118 | ENST00000650611.1 | n.173-38663G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000894 AC: 136AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251090Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135682
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461836Hom.: 0 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 727212
GnomAD4 genome AF: 0.000919 AC: 140AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.000954 AC XY: 71AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.126G>C (p.E42D) alteration is located in exon 2 (coding exon 1) of the SOCS5 gene. This alteration results from a G to C substitution at nucleotide position 126, causing the glutamic acid (E) at amino acid position 42 to be replaced by an aspartic acid (D). 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