rs137921473
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The ENST00000374695.8(HSPG2):c.9789C>T(p.Leu3263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L3263L) has been classified as Likely benign.
Frequency
Consequence
ENST00000374695.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPG2 | NM_005529.7 | c.9789C>T | p.Leu3263= | synonymous_variant | 73/97 | ENST00000374695.8 | NP_005520.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSPG2 | ENST00000374695.8 | c.9789C>T | p.Leu3263= | synonymous_variant | 73/97 | 1 | NM_005529.7 | ENSP00000363827 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 250942Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135726
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461784Hom.: 0 Cov.: 35 AF XY: 0.0000619 AC XY: 45AN XY: 727190
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at