rs13179769

Positions:

• chr5-136158171-C-A
• chr5-136158171-C-G

Variant summary

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

The NM_005903.7(SMAD5):​c.404-2685C>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 151,736 control chromosomes in the GnomAD database, including 10,837 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 (10837 hom., cov: 31)
• Consequence: SMAD5 NM_005903.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

SMAD5 (HGNC:6771): (SMAD family member 5) The protein encoded by this gene is involved in the transforming growth factor beta signaling pathway that results in an inhibition of the proliferation of hematopoietic progenitor cells. The encoded protein is activated by bone morphogenetic proteins type 1 receptor kinase, and may be involved in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMAD5	NM_005903.7	c.404-2685C>A		intron_variant		ENST00000545279.6	NP_005894.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAD5	ENST00000545279.6	c.404-2685C>A		intron_variant		1	NM_005903.7	ENSP00000441954.2
SMAD5	ENST00000509297.6	c.404-2685C>A		intron_variant		1		ENSP00000426696.2
SMAD5	ENST00000545620.5	c.404-2685C>A		intron_variant		5		ENSP00000446474.2
SMAD5	ENST00000514777.1	n.60-14263C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54639 AN: 151618 Hom.: 10808 Cov.: 31

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.361 AC: 54714 AN: 151736 Hom.: 10837 Cov.: 31 AF XY: 0.356 AC XY: 26418 AN XY: 74152

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.384

Alfa AF: 0.327 Hom.: 1439

Bravo AF: 0.374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.54

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: rs13179769; hg19: chr5-135493860;