17-18335678-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004169.5(SHMT1):c.815-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,602,138 control chromosomes in the GnomAD database, including 24 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_004169.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHMT1 | NM_004169.5 | c.815-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000316694.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHMT1 | ENST00000316694.8 | c.815-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004169.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00556 AC: 846AN: 152146Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.00161 AC: 404AN: 251496Hom.: 3 AF XY: 0.00126 AC XY: 171AN XY: 135922
GnomAD4 exome AF: 0.000759 AC: 1100AN: 1449874Hom.: 12 Cov.: 27 AF XY: 0.000661 AC XY: 477AN XY: 722164
GnomAD4 genome ? AF: 0.00558 AC: 849AN: 152264Hom.: 12 Cov.: 33 AF XY: 0.00556 AC XY: 414AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at