rs11071933

chr15-67109408-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005902.4(SMAD3):c.206+43048G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,882 control chromosomes in the GnomAD database, including 23,206 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 0.52 (23206 hom., cov: 30)
• Consequence: SMAD3 NM_005902.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

Genes affected

SMAD3 (HGNC:6769): (SMAD family member 3) The SMAD family of proteins are a group of intracellular signal transducer proteins similar to the gene products of the Drosophila gene 'mothers against decapentaplegic' (Mad) and the C. elegans gene Sma. The SMAD3 protein functions in the transforming growth factor-beta signaling pathway, and transmits signals from the cell surface to the nucleus, regulating gene activity and cell proliferation. This protein forms a complex with other SMAD proteins and binds DNA, functioning both as a transcription factor and tumor suppressor. Mutations in this gene are associated with aneurysms-osteoarthritis syndrome and Loeys-Dietz Syndrome 3. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAD3	NM_005902.4	c.206+43048G>C		intron_variant		ENST00000327367.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAD3	ENST00000327367.9	c.206+43048G>C		intron_variant		1	NM_005902.4	P1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78388 AN: 151764 Hom.: 23209 Cov.: 30

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.516 AC: 78385 AN: 151882 Hom.: 23206 Cov.: 30 AF XY: 0.515 AC XY: 38187 AN XY: 74210

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.528

Alfa AF: 0.590 Hom.: 3551

Bravo AF: 0.486

Asia WGS AF: 0.380 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	5.6
Dann	Benign	0.55

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: rs11071933; hg19: chr15-67401746;