chr12-6974427-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_006331.8(EMG1):āc.257A>Gā(p.Asp86Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. D86D) has been classified as Likely benign.
Frequency
Consequence
NM_006331.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMG1 | NM_006331.8 | c.257A>G | p.Asp86Gly | missense_variant | 2/6 | ENST00000599672.6 | |
EMG1 | NM_001320049.2 | c.257A>G | p.Asp86Gly | missense_variant | 2/5 | ||
EMG1 | NR_135131.2 | n.268A>G | non_coding_transcript_exon_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMG1 | ENST00000599672.6 | c.257A>G | p.Asp86Gly | missense_variant | 2/6 | 1 | NM_006331.8 | P1 | |
EMG1 | ENST00000539196.2 | c.122A>G | p.Asp41Gly | missense_variant | 2/5 | 2 | |||
EMG1 | ENST00000611981.1 | n.268A>G | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
EMG1 | ENST00000620255.1 | n.246A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248786Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135010
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461390Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726952
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
Bowen-Conradi syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at