15-67069436-G-A

Position:

• chr15-67069436-G-A

Variant summary

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

The ENST00000327367.9(SMAD3):​c.206+3076G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,932 control chromosomes in the GnomAD database, including 10,168 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 0.36 (10168 hom., cov: 31)
• Consequence: SMAD3 ENST00000327367.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMAD3	NM_005902.4	c.206+3076G>A		intron_variant		ENST00000327367.9	NP_005893.1
SMAD3	NM_001407011.1	c.206+3076G>A		intron_variant			NP_001393940.1
SMAD3	NM_001407012.1	c.206+3076G>A		intron_variant			NP_001393941.1
SMAD3	NM_001407013.1	c.206+3076G>A		intron_variant			NP_001393942.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAD3	ENST00000327367.9	c.206+3076G>A		intron_variant		1	NM_005902.4	ENSP00000332973	P1
SMAD3	ENST00000559460.6	c.-110+5492G>A		intron_variant		4		ENSP00000453082
SMAD3	ENST00000560424.2	c.206+3076G>A		intron_variant		3		ENSP00000455540
SMAD3	ENST00000679624.1	c.-110+1523G>A		intron_variant				ENSP00000505445

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54716 AN: 151814 Hom.: 10140 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.361 AC: 54782 AN: 151932 Hom.: 10168 Cov.: 31 AF XY: 0.363 AC XY: 26979 AN XY: 74252

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.352

Alfa AF: 0.342 Hom.: 2542

Bravo AF: 0.345

Asia WGS AF: 0.494 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.68

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: rs12904944; hg19: chr15-67361774;