chr7-74028193-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000501.4(ELN):c.6G>A(p.Ala2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A2A) has been classified as Likely benign.
Frequency
Consequence
NM_000501.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELN | NM_000501.4 | c.6G>A | p.Ala2= | synonymous_variant | 1/33 | ENST00000252034.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELN | ENST00000252034.12 | c.6G>A | p.Ala2= | synonymous_variant | 1/33 | 1 | NM_000501.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151610Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000329 AC: 8AN: 243266Hom.: 0 AF XY: 0.0000527 AC XY: 7AN XY: 132890
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1459614Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726124
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151610Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74042
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | - - |
Supravalvar aortic stenosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at