19-14743421-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_013447.4(ADGRE2):c.2462C>T(p.Thr821Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00865 in 1,613,330 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. T821T) has been classified as Uncertain significance.
Frequency
Consequence
NM_013447.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRE2 | NM_013447.4 | c.2462C>T | p.Thr821Met | missense_variant, splice_region_variant | 20/21 | ENST00000315576.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRE2 | ENST00000315576.8 | c.2462C>T | p.Thr821Met | missense_variant, splice_region_variant | 20/21 | 1 | NM_013447.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00623 AC: 948AN: 152142Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.00631 AC: 1585AN: 251266Hom.: 7 AF XY: 0.00637 AC XY: 865AN XY: 135766
GnomAD4 exome AF: 0.00890 AC: 13001AN: 1461070Hom.: 66 Cov.: 31 AF XY: 0.00892 AC XY: 6483AN XY: 726924
GnomAD4 genome AF: 0.00623 AC: 948AN: 152260Hom.: 6 Cov.: 31 AF XY: 0.00583 AC XY: 434AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at