rs4042056
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000641136.1(IGHG3):c.1094G>A(p.Arg365His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.097 ( 165 hom., cov: 31)
Exomes 𝑓: 0.031 ( 1362 hom. )
Failed GnomAD Quality Control
Consequence
IGHG3
ENST00000641136.1 missense
ENST00000641136.1 missense
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.662
Genes affected
IGHG3 (HGNC:5527): (immunoglobulin heavy constant gamma 3 (G3m marker)) Predicted to enable antigen binding activity and immunoglobulin receptor binding activity. Involved in retina homeostasis. Located in blood microparticle and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGHG3 | ENST00000641136.1 | c.1094G>A | p.Arg365His | missense_variant | 7/9 | P5 | |||
IGHG3 | ENST00000390551.6 | c.1094G>A | p.Arg365His | missense_variant | 7/7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0971 AC: 10827AN: 111498Hom.: 162 Cov.: 31
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GnomAD4 exome AF: 0.0306 AC: 18364AN: 600176Hom.: 1362 Cov.: 0 AF XY: 0.0334 AC XY: 10946AN XY: 327884
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0973 AC: 10853AN: 111546Hom.: 165 Cov.: 31 AF XY: 0.104 AC XY: 5626AN XY: 54138
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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