chr12-96259860-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005230.4(ELK3):c.1125+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000823 in 1,586,442 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005230.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
ELK3 | NM_005230.4 | c.1125+7G>A | splice_region_variant, intron_variant | ENST00000228741.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELK3 | ENST00000228741.8 | c.1125+7G>A | splice_region_variant, intron_variant | 1 | NM_005230.4 | P1 | |||
ELK3 | ENST00000552142.5 | c.330+7G>A | splice_region_variant, intron_variant | 5 | |||||
ELK3 | ENST00000549985.1 | c.*101+7G>A | splice_region_variant, intron_variant, NMD_transcript_variant | 3 | |||||
ELK3 | ENST00000549529.1 | n.214+7G>A | splice_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00436 AC: 664AN: 152208Hom.: 13 Cov.: 33
GnomAD3 exomes AF: 0.00128 AC: 298AN: 231996Hom.: 5 AF XY: 0.000874 AC XY: 110AN XY: 125874
GnomAD4 exome AF: 0.000447 AC: 641AN: 1434116Hom.: 7 Cov.: 32 AF XY: 0.000391 AC XY: 279AN XY: 712814
GnomAD4 genome AF: 0.00436 AC: 664AN: 152326Hom.: 13 Cov.: 33 AF XY: 0.00411 AC XY: 306AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at