chr19-3151816-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002068.4(GNA15):c.595G>A(p.Val199Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,611,470 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 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.595G>A | p.Val199Met | missense_variant | 4/7 | ENST00000262958.4 | |
GNA15-DT | NR_110670.1 | n.159-2026C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNA15 | ENST00000262958.4 | c.595G>A | p.Val199Met | missense_variant | 4/7 | 1 | NM_002068.4 | P1 | |
GNA15-DT | ENST00000587587.1 | n.159-2026C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
GNA15 | ENST00000586082.1 | n.556G>A | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
GNA15 | ENST00000592455.1 | c.*625G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000725 AC: 18AN: 248374Hom.: 1 AF XY: 0.0000669 AC XY: 9AN XY: 134616
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1459266Hom.: 1 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 726020
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.595G>A (p.V199M) alteration is located in exon 4 (coding exon 4) of the GNA15 gene. This alteration results from a G to A substitution at nucleotide position 595, causing the valine (V) at amino acid position 199 to be replaced by a methionine (M). 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