chr2-99018545-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025244.4(TSGA10):c.1913G>T(p.Arg638Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000822 in 1,460,480 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R638H) has been classified as Uncertain significance.
Frequency
Consequence
NM_025244.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSGA10 | NM_025244.4 | c.1913G>T | p.Arg638Leu | missense_variant | 19/21 | ENST00000393483.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSGA10 | ENST00000393483.8 | c.1913G>T | p.Arg638Leu | missense_variant | 19/21 | 1 | NM_025244.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249632Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134932
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460480Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726476
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2024 | The c.1913G>T (p.R638L) alteration is located in exon 19 (coding exon 14) of the TSGA10 gene. This alteration results from a G to T substitution at nucleotide position 1913, causing the arginine (R) at amino acid position 638 to be replaced by a leucine (L). 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