5-136181231-A-G

Position:

• chr5-136181231-A-G

Variant summary

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

The NM_005903.7(SMAD5):​c.*3751A>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 0.355 in 151,952 control chromosomes in the GnomAD database, including 10,411 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 (10411 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SMAD5 NM_005903.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAD5	NM_005903.7	c.*3751A>G		3_prime_UTR_variant	8/8	ENST00000545279.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAD5	ENST00000545279.6	c.*3751A>G		3_prime_UTR_variant	8/8	1	NM_005903.7	P1
SMAD5	ENST00000545620.5	c.*3751A>G		3_prime_UTR_variant	7/7	5		P1
SMAD5	ENST00000513418.1	c.165-5930A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53878 AN: 151832 Hom.: 10389 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.382

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.355 AC: 53944 AN: 151952 Hom.: 10411 Cov.: 32 AF XY: 0.351 AC XY: 26048 AN XY: 74276

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.384

Alfa AF: 0.337 Hom.: 1364

Bravo AF: 0.368

Asia WGS AF: 0.341 AC: 1187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.46

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: rs6871224; hg19: chr5-135516919;