chr12-6970961-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006331.8(EMG1):c.38G>T(p.Arg13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,613,054 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006331.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMG1 | NM_006331.8 | c.38G>T | p.Arg13Leu | missense_variant | 1/6 | ENST00000599672.6 | |
EMG1 | NM_001320049.2 | c.38G>T | p.Arg13Leu | missense_variant | 1/5 | ||
EMG1 | NR_135131.2 | n.49G>T | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMG1 | ENST00000599672.6 | c.38G>T | p.Arg13Leu | missense_variant | 1/6 | 1 | NM_006331.8 | P1 | |
EMG1 | ENST00000611981.1 | n.49G>T | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
EMG1 | ENST00000620255.1 | n.27G>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00789 AC: 1201AN: 152194Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00198 AC: 488AN: 246618Hom.: 10 AF XY: 0.00140 AC XY: 188AN XY: 133848
GnomAD4 exome AF: 0.000785 AC: 1146AN: 1460742Hom.: 19 Cov.: 32 AF XY: 0.000650 AC XY: 472AN XY: 726564
GnomAD4 genome AF: 0.00797 AC: 1214AN: 152312Hom.: 12 Cov.: 32 AF XY: 0.00753 AC XY: 561AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 10, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at