rs12654591
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_152403.4(EGFLAM):c.97+12629C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 152,226 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.017 ( 47 hom., cov: 33)
Consequence
EGFLAM
NM_152403.4 intron
NM_152403.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0190
Genes affected
EGFLAM (HGNC:26810): (EGF like, fibronectin type III and laminin G domains) Predicted to enable calcium ion binding activity and glycosaminoglycan binding activity. Predicted to be involved in animal organ morphogenesis and tissue development. Predicted to act upstream of or within extracellular matrix organization; peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan; and positive regulation of cell-substrate adhesion. Part of cell surface. [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=-0.72).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0175 (2660/152226) while in subpopulation EAS AF= 0.0456 (236/5170). AF 95% confidence interval is 0.0409. There are 47 homozygotes in gnomad4. There are 1331 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 47 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGFLAM | NM_152403.4 | c.97+12629C>A | intron_variant | ENST00000322350.10 | |||
EGFLAM | NM_001205301.2 | c.97+12629C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGFLAM | ENST00000322350.10 | c.97+12629C>A | intron_variant | 1 | NM_152403.4 | P3 | |||
EGFLAM | ENST00000354891.7 | c.97+12629C>A | intron_variant | 1 | A2 | ||||
EGFLAM | ENST00000504709.1 | c.97+12629C>A | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0175 AC: 2660AN: 152108Hom.: 47 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0175 AC: 2660AN: 152226Hom.: 47 Cov.: 33 AF XY: 0.0179 AC XY: 1331AN XY: 74428
GnomAD4 genome
?
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33
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1331
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74428
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113
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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