chr1-21839471-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005529.7(HSPG2):c.9789C>A(p.Leu3263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000429 in 1,614,096 control chromosomes in the GnomAD database, including 3 homozygotes. 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
NM_005529.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPG2 | NM_005529.7 | c.9789C>A | p.Leu3263= | synonymous_variant | 73/97 | ENST00000374695.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPG2 | ENST00000374695.8 | c.9789C>A | p.Leu3263= | synonymous_variant | 73/97 | 1 | NM_005529.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 337AN: 152198Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000626 AC: 157AN: 250942Hom.: 1 AF XY: 0.000494 AC XY: 67AN XY: 135726
GnomAD4 exome AF: 0.000244 AC: 356AN: 1461780Hom.: 2 Cov.: 35 AF XY: 0.000221 AC XY: 161AN XY: 727186
GnomAD4 genome AF: 0.00221 AC: 337AN: 152316Hom.: 1 Cov.: 33 AF XY: 0.00193 AC XY: 144AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 28, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jan 29, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 22, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 08, 2016 | - - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Sep 30, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at