chr1-163069317-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000421743.6(RGS4):c.124G>T(p.Gly42Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,551,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000421743.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS4 | NM_001102445.3 | c.124G>T | p.Gly42Cys | missense_variant | 2/6 | ||
RGS4 | NM_001113381.1 | c.-168G>T | 5_prime_UTR_variant | 1/4 | |||
RGS4 | NM_005613.6 | upstream_gene_variant | ENST00000367909.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS4 | ENST00000367909.11 | upstream_gene_variant | 1 | NM_005613.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000961 AC: 15AN: 156114Hom.: 0 AF XY: 0.000109 AC XY: 9AN XY: 82334
GnomAD4 exome AF: 0.0000193 AC: 27AN: 1399234Hom.: 0 Cov.: 33 AF XY: 0.0000217 AC XY: 15AN XY: 690190
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.124G>T (p.G42C) alteration is located in exon 2 (coding exon 2) of the RGS4 gene. This alteration results from a G to T substitution at nucleotide position 124, causing the glycine (G) at amino acid position 42 to be replaced by a cysteine (C). 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