rs9304407

Positions:

• chr18-51069023-C-G

Variant summary

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

The NM_005359.6(SMAD4):​c.1308+1836C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,042 control chromosomes in the GnomAD database, including 25,747 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 0.54 (25747 hom., cov: 32)
• Consequence: SMAD4 NM_005359.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

SMAD4 (HGNC:6770): (SMAD family member 4) This gene encodes a member of the Smad family of signal transduction proteins. Smad proteins are phosphorylated and activated by transmembrane serine-threonine receptor kinases in response to transforming growth factor (TGF)-beta signaling. The product of this gene forms homomeric complexes and heteromeric complexes with other activated Smad proteins, which then accumulate in the nucleus and regulate the transcription of target genes. This protein binds to DNA and recognizes an 8-bp palindromic sequence (GTCTAGAC) called the Smad-binding element (SBE). The protein acts as a tumor suppressor and inhibits epithelial cell proliferation. It may also have an inhibitory effect on tumors by reducing angiogenesis and increasing blood vessel hyperpermeability. The encoded protein is a crucial component of the bone morphogenetic protein signaling pathway. The Smad proteins are subject to complex regulation by post-translational modifications. Mutations or deletions in this gene have been shown to result in pancreatic cancer, juvenile polyposis syndrome, and hereditary hemorrhagic telangiectasia syndrome. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAD4	NM_005359.6	c.1308+1836C>G		intron_variant		ENST00000342988.8
SMAD4	NM_001407041.1	c.1308+1836C>G		intron_variant
SMAD4	NM_001407042.1	c.1308+1836C>G		intron_variant
SMAD4	NR_176265.1	n.1846+1836C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAD4	ENST00000342988.8	c.1308+1836C>G		intron_variant		5	NM_005359.6	P1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82119 AN: 151924 Hom.: 25683 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.541 AC: 82248 AN: 152042 Hom.: 25747 Cov.: 32 AF XY: 0.537 AC XY: 39867 AN XY: 74304

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.512

Alfa AF: 0.470 Hom.: 2440

Bravo AF: 0.568

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.60

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: rs9304407; hg19: chr18-48595393;