5-54981998-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_007036.5(ESM1):c.450G>A(p.Thr150=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,613,780 control chromosomes in the GnomAD database, including 154 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_007036.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESM1 | NM_007036.5 | c.450G>A | p.Thr150= | splice_region_variant, synonymous_variant | 2/3 | ENST00000381405.5 | |
ESM1 | NM_001135604.2 | c.302-2563G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESM1 | ENST00000381405.5 | c.450G>A | p.Thr150= | splice_region_variant, synonymous_variant | 2/3 | 1 | NM_007036.5 | P1 | |
ESM1 | ENST00000381403.4 | c.302-2563G>A | intron_variant | 1 | |||||
ESM1 | ENST00000598310.5 | n.230-2563G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00836 AC: 1272AN: 152152Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00936 AC: 2352AN: 251224Hom.: 18 AF XY: 0.00988 AC XY: 1342AN XY: 135778
GnomAD4 exome AF: 0.0117 AC: 17159AN: 1461510Hom.: 144 Cov.: 30 AF XY: 0.0116 AC XY: 8463AN XY: 727090
GnomAD4 genome AF: 0.00835 AC: 1272AN: 152270Hom.: 10 Cov.: 32 AF XY: 0.00856 AC XY: 637AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 19, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at