rs779853780
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001271938.2(MEGF8):āc.6064A>Cā(p.Thr2022Pro) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T2022A) has been classified as Uncertain significance.
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 32)
Exomes š: 0.000041 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MEGF8
NM_001271938.2 missense
NM_001271938.2 missense
Scores
2
6
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.07
Genes affected
MEGF8 (HGNC:3233): (multiple EGF like domains 8) The protein encoded by this gene is a single-pass type I membrane protein of unknown function that contains several EGF-like domains, Kelch repeats, and PSI domains. Defects in this gene are a cause of Carpenter syndrome 2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.15899652).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEGF8 | NM_001271938.2 | c.6064A>C | p.Thr2022Pro | missense_variant | 35/42 | ENST00000251268.11 | |
MEGF8 | NM_001410.3 | c.5863A>C | p.Thr1955Pro | missense_variant | 34/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEGF8 | ENST00000251268.11 | c.6064A>C | p.Thr2022Pro | missense_variant | 35/42 | 5 | NM_001271938.2 | A2 | |
MEGF8 | ENST00000334370.8 | c.5863A>C | p.Thr1955Pro | missense_variant | 34/41 | 1 | P2 | ||
MEGF8 | ENST00000378073.5 | c.-1022A>C | 5_prime_UTR_variant | 35/41 | 5 | ||||
MEGF8 | ENST00000598762.1 | c.161+840A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 4AN: 150870Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 genomes
?
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150870
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32
FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000407 AC: 59AN: 1450992Hom.: 0 Cov.: 33 AF XY: 0.0000430 AC XY: 31AN XY: 721076
GnomAD4 exome
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000331 AC: 5AN: 150970Hom.: 0 Cov.: 32 AF XY: 0.0000543 AC XY: 4AN XY: 73638
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Data not reliable, filtered out with message: AS_VQSR
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ExAC
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31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Benign
T;D
Sift4G
Uncertain
D;D
Polyphen
D;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at