1-30873045-G-C

Variant names:

• chr1-30873045-G-C
• rs3766285
• NM_014654.4:c.*166C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014654.4(SDC3):​c.*166C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000611 in 491,194 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000061 (0 hom.)
• Consequence: SDC3 NM_014654.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 5 publications found

Genes affected

SDC3 (HGNC:10660): (syndecan 3) The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014654.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC3	NM_014654.4	MANE Select	c.*166C>G		3_prime_UTR	Exon 5 of 5	NP_055469.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDC3	ENST00000339394.7	TSL:1 MANE Select	c.*166C>G		3_prime_UTR	Exon 5 of 5	ENSP00000344468.6	O75056
	SDC3	ENST00000336798.11	TSL:1	c.*166C>G		3_prime_UTR	Exon 3 of 3	ENSP00000338346.7	A0A9K3Y886
	SDC3	ENST00000937355.1		c.*166C>G		3_prime_UTR	Exon 5 of 5	ENSP00000607414.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000611 AC: 3 AN: 491194 Hom.: 0 Cov.: 4 AF XY: 0.00000383 AC XY: 1 AN XY: 261350

African (AFR) AF: 0.00 AC: 0 AN: 13726

American (AMR) AF: 0.00 AC: 0 AN: 21668

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14054

East Asian (EAS) AF: 0.0000300 AC: 1 AN: 33316

South Asian (SAS) AF: 0.00 AC: 0 AN: 49636

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38792

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2024

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 290470

Other (OTH) AF: 0.0000727 AC: 2 AN: 27508

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 878

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.48
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3766285; hg19: chr1-31345892;