rs777831498
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001271938.2(MEGF8):āc.1791T>Cā(p.Cys597=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000245 in 1,588,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001271938.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEGF8 | NM_001271938.2 | c.1791T>C | p.Cys597= | splice_region_variant, synonymous_variant | 11/42 | ENST00000251268.11 | |
MEGF8 | NM_001410.3 | c.1791T>C | p.Cys597= | splice_region_variant, synonymous_variant | 11/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEGF8 | ENST00000251268.11 | c.1791T>C | p.Cys597= | splice_region_variant, synonymous_variant | 11/42 | 5 | NM_001271938.2 | A2 | |
MEGF8 | ENST00000334370.8 | c.1791T>C | p.Cys597= | splice_region_variant, synonymous_variant | 11/41 | 1 | P2 | ||
MEGF8 | ENST00000378073.5 | c.-5295T>C | splice_region_variant, 5_prime_UTR_variant | 11/41 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000354 AC: 8AN: 225910Hom.: 0 AF XY: 0.0000162 AC XY: 2AN XY: 123678
GnomAD4 exome AF: 0.0000265 AC: 38AN: 1436630Hom.: 0 Cov.: 31 AF XY: 0.0000238 AC XY: 17AN XY: 714374
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
MEGF8-related Carpenter syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at