chr19-3136498-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002068.4(GNA15):c.48G>C(p.Glu16Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000385 in 1,558,962 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_002068.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNA15 | NM_002068.4 | c.48G>C | p.Glu16Asp | missense_variant | 1/7 | ENST00000262958.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNA15 | ENST00000262958.4 | c.48G>C | p.Glu16Asp | missense_variant | 1/7 | 1 | NM_002068.4 | P1 | |
GNA15 | ENST00000592455.1 | c.48G>C | p.Glu16Asp | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000178 AC: 3AN: 168072Hom.: 0 AF XY: 0.0000224 AC XY: 2AN XY: 89368
GnomAD4 exome AF: 0.0000391 AC: 55AN: 1406790Hom.: 0 Cov.: 32 AF XY: 0.0000345 AC XY: 24AN XY: 694766
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.48G>C (p.E16D) alteration is located in exon 1 (coding exon 1) of the GNA15 gene. This alteration results from a G to C substitution at nucleotide position 48, causing the glutamic acid (E) at amino acid position 16 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