chr20-45336885-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_002999.4(SDC4):c.61-965T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 152,036 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0040 ( 16 hom., cov: 31)
Consequence
SDC4
NM_002999.4 intron
NM_002999.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.407
Genes affected
SDC4 (HGNC:10661): (syndecan 4) The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan that functions as a receptor in intracellular signaling. The encoded protein is found as a homodimer and is a member of the syndecan proteoglycan family. This gene is found on chromosome 20, while a pseudogene has been found on chromosome 22. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 20-45336885-A-G is Benign according to our data. Variant chr20-45336885-A-G is described in ClinVar as [Benign]. Clinvar id is 444109.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00402 (611/152036) while in subpopulation AMR AF= 0.0288 (440/15268). AF 95% confidence interval is 0.0266. There are 16 homozygotes in gnomad4. There are 313 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 15 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDC4 | NM_002999.4 | c.61-965T>C | intron_variant | ENST00000372733.3 | |||
SDC4 | XM_011528977.3 | c.-17-3816T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDC4 | ENST00000372733.3 | c.61-965T>C | intron_variant | 1 | NM_002999.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00400 AC: 607AN: 151918Hom.: 15 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00402 AC: 611AN: 152036Hom.: 16 Cov.: 31 AF XY: 0.00421 AC XY: 313AN XY: 74334
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Type 2 diabetes mellitus Benign:1
Benign, no assertion criteria provided | case-control | Diabetes Molecular Genetics Section, Phoenix Epidemiology and Clinical Research Branch, National Institutes of Health | - | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at