20-45340366-CT-C

Position:

• chr20-45340366-CT-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_002999.4(SDC4):​c.61-4447del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 152,302 control chromosomes in the GnomAD database, including 72 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.010 (72 hom., cov: 33)
• Consequence: SDC4 NM_002999.4 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.400

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 20-45340366-CT-C is Benign according to our data. Variant chr20-45340366-CT-C is described in ClinVar as [Benign]. Clinvar id is 444115.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDC4	NM_002999.4	c.61-4447del		intron_variant		ENST00000372733.3	NP_002990.2
SDC4	XM_011528977.3	c.-17-7298del		intron_variant			XP_011527279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDC4	ENST00000372733.3	c.61-4447del		intron_variant		1	NM_002999.4	ENSP00000361818	P1

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1542 AN: 152184 Hom.: 70 Cov.: 33

Gnomad AFR AF: 0.00212

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.0120

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0102 AC: 1553 AN: 152302 Hom.: 72 Cov.: 33 AF XY: 0.0115 AC XY: 855 AN XY: 74472

Gnomad4 AFR AF: 0.00212

Gnomad4 AMR AF: 0.0734

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0565

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.00569 Hom.: 2

Bravo AF: 0.0154

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

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

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs148973596; hg19: chr20-43969006;