19-2276297-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198532.3(PEAK3):c.805G>A(p.Ala269Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,592,630 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198532.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEAK3 | NM_198532.3 | c.805G>A | p.Ala269Thr | missense_variant | Exon 4 of 4 | ENST00000342063.5 | NP_940934.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEAK3 | ENST00000342063.5 | c.805G>A | p.Ala269Thr | missense_variant | Exon 4 of 4 | 2 | NM_198532.3 | ENSP00000345102.3 | ||
ENSG00000273734 | ENST00000621615.1 | n.146+6553C>T | intron_variant | Intron 1 of 7 | 2 | ENSP00000481965.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000282 AC: 59AN: 209040Hom.: 1 AF XY: 0.000402 AC XY: 47AN XY: 116912
GnomAD4 exome AF: 0.000165 AC: 237AN: 1440294Hom.: 4 Cov.: 31 AF XY: 0.000267 AC XY: 191AN XY: 716442
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.805G>A (p.A269T) alteration is located in exon 4 (coding exon 3) of the C19orf35 gene. This alteration results from a G to A substitution at nucleotide position 805, causing the alanine (A) at amino acid position 269 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