rs1131351

Variant names:

• chr2-20202619-C-G
• rs1131351
• NM_002997.5:c.*147G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-20202619-C-G
• chr2-20202619-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002997.5(SDC1):​c.*147G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 773,762 control chromosomes in the GnomAD database, including 74,640 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.40 (12632 hom., cov: 31)
  • Exomes 𝑓: 0.44 (62008 hom.)
• Consequence: SDC1 NM_002997.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 16 publications found

Genes affected

SDC1 (HGNC:10658): (syndecan 1) The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002997.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC1	NM_002997.5	MANE Select	c.*147G>C		3_prime_UTR	Exon 5 of 5	NP_002988.4
	SDC1	NM_001006946.2		c.*147G>C		3_prime_UTR	Exon 6 of 6	NP_001006947.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC1	ENST00000254351.9	TSL:1 MANE Select	c.*147G>C		3_prime_UTR	Exon 5 of 5	ENSP00000254351.4
	SDC1	ENST00000403076.5	TSL:1	c.479-318G>C		intron	N/A	ENSP00000384613.1
	SDC1	ENST00000381150.5	TSL:5	c.*147G>C		3_prime_UTR	Exon 6 of 6	ENSP00000370542.1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60268 AN: 151902 Hom.: 12616 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.383

GnomAD4 exome AF: 0.443 AC: 275546 AN: 621740 Hom.: 62008 Cov.: 8 AF XY: 0.442 AC XY: 143845 AN XY: 325178

African (AFR) AF: 0.268 AC: 4312 AN: 16110

American (AMR) AF: 0.433 AC: 11454 AN: 26472

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 5572 AN: 15138

East Asian (EAS) AF: 0.378 AC: 13221 AN: 34976

South Asian (SAS) AF: 0.433 AC: 22435 AN: 51850

European-Finnish (FIN) AF: 0.554 AC: 21806 AN: 39362

Middle Eastern (MID) AF: 0.310 AC: 745 AN: 2404

European-Non Finnish (NFE) AF: 0.452 AC: 182313 AN: 403584

Other (OTH) AF: 0.430 AC: 13688 AN: 31844

GnomAD4 genome AF: 0.397 AC: 60314 AN: 152022 Hom.: 12632 Cov.: 31 AF XY: 0.404 AC XY: 30040 AN XY: 74298

African (AFR) AF: 0.265 AC: 10992 AN: 41468

American (AMR) AF: 0.401 AC: 6123 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2111 AN: 5142

South Asian (SAS) AF: 0.452 AC: 2174 AN: 4812

European-Finnish (FIN) AF: 0.575 AC: 6075 AN: 10566

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30342 AN: 67968

Other (OTH) AF: 0.379 AC: 801 AN: 2112

Alfa AF: 0.302 Hom.: 898

Bravo AF: 0.380

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.3
DANN	Benign	0.88
PhyloP100		-0.040
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1131351; hg19: chr2-20402380; COSMIC: COSV54342223; COSMIC: COSV54342223;