X-47637043-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000343894.8(ELK1):c.280G>A(p.Ala94Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0008 in 1,208,342 control chromosomes in the GnomAD database, including 3 homozygotes. There are 280 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000343894.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELK1 | NM_001114123.3 | c.1158G>A | p.Ala386= | synonymous_variant | 6/7 | ENST00000376983.8 | |
ELK1 | NM_001257168.1 | c.280G>A | p.Ala94Thr | missense_variant | 5/6 | ||
ELK1 | NM_005229.4 | c.1158G>A | p.Ala386= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELK1 | ENST00000343894.8 | c.280G>A | p.Ala94Thr | missense_variant | 5/6 | 1 | |||
ELK1 | ENST00000376983.8 | c.1158G>A | p.Ala386= | synonymous_variant | 6/7 | 1 | NM_001114123.3 | P1 | |
ELK1 | ENST00000247161.7 | c.1158G>A | p.Ala386= | synonymous_variant | 5/6 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00438 AC: 487AN: 111087Hom.: 1 Cov.: 22 AF XY: 0.00387 AC XY: 129AN XY: 33335
GnomAD3 exomes AF: 0.00122 AC: 218AN: 178934Hom.: 2 AF XY: 0.000808 AC XY: 52AN XY: 64362
GnomAD4 exome AF: 0.000437 AC: 480AN: 1097203Hom.: 2 Cov.: 31 AF XY: 0.000414 AC XY: 150AN XY: 362663
GnomAD4 genome AF: 0.00438 AC: 487AN: 111139Hom.: 1 Cov.: 22 AF XY: 0.00389 AC XY: 130AN XY: 33397
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at