chr10-17660546-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_003473.4(STAM):āc.123T>Cā(p.Thr41=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,588,300 control chromosomes in the GnomAD database, including 135 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 (ā ).
Frequency
Consequence
NM_003473.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAM | NM_003473.4 | c.123T>C | p.Thr41= | splice_region_variant, synonymous_variant | 2/14 | ENST00000377524.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAM | ENST00000377524.8 | c.123T>C | p.Thr41= | splice_region_variant, synonymous_variant | 2/14 | 1 | NM_003473.4 | P1 | |
STAM | ENST00000377500.1 | c.-37+16167T>C | intron_variant | 5 | |||||
STAM | ENST00000445846.1 | c.123T>C | p.Thr41= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 2/7 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00826 AC: 1257AN: 152192Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.0105 AC: 2221AN: 211064Hom.: 19 AF XY: 0.0115 AC XY: 1322AN XY: 115186
GnomAD4 exome AF: 0.0115 AC: 16532AN: 1435990Hom.: 124 Cov.: 29 AF XY: 0.0119 AC XY: 8479AN XY: 714360
GnomAD4 genome AF: 0.00825 AC: 1257AN: 152310Hom.: 11 Cov.: 32 AF XY: 0.00808 AC XY: 602AN XY: 74470
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