chr10-2501620-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The XM_011519770.3(LOC107983989):c.328G>A(p.Val110Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00661 in 146,682 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
XM_011519770.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC02645 | ENST00000414107.6 | n.96G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
LINC02645 | ENST00000662131.1 | n.150G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||||
ENSG00000235281 | ENST00000664280.1 | n.21C>T | non_coding_transcript_exon_variant | Exon 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00662 AC: 970AN: 146586Hom.: 15 Cov.: 27
GnomAD4 genome AF: 0.00661 AC: 970AN: 146682Hom.: 15 Cov.: 27 AF XY: 0.00658 AC XY: 471AN XY: 71606
ClinVar
Submissions by phenotype
not provided Benign:1
ENSG00000235281: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at