chrX-136344704-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_153834.4(ADGRG4):āc.998T>Cā(p.Ile333Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,202,023 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_153834.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRG4 | NM_153834.4 | c.998T>C | p.Ile333Thr | missense_variant | 6/26 | ENST00000394143.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRG4 | ENST00000394143.6 | c.998T>C | p.Ile333Thr | missense_variant | 6/26 | 1 | NM_153834.4 | P1 | |
ADGRG4 | ENST00000394141.1 | c.383T>C | p.Ile128Thr | missense_variant | 3/23 | 1 | |||
ADGRG4 | ENST00000370652.5 | c.998T>C | p.Ile333Thr | missense_variant | 4/24 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 3AN: 111724Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33948
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181967Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66935
GnomAD4 exome AF: 0.0000119 AC: 13AN: 1090299Hom.: 0 Cov.: 32 AF XY: 0.0000112 AC XY: 4AN XY: 356049
GnomAD4 genome AF: 0.0000269 AC: 3AN: 111724Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33948
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.998T>C (p.I333T) alteration is located in exon 6 (coding exon 3) of the ADGRG4 gene. This alteration results from a T to C substitution at nucleotide position 998, causing the isoleucine (I) at amino acid position 333 to be replaced by a threonine (T). 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