ENST00000558071.2:n.114+30092A>G

Variant names:

• chr15-67029048-T-C
• rs7178347
• ENST00000558071.2:n.114+30092A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558071.2(SMAD3-DT):​n.114+30092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,982 control chromosomes in the GnomAD database, including 33,515 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 0.66 (33515 hom., cov: 31)
• Consequence: SMAD3-DT ENST00000558071.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

Genes affected

SMAD3-DT (HGNC:56759): (SMAD3 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558071.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD3-DT	NR_135686.1		n.1140+30092A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD3-DT	ENST00000558071.2	TSL:5	n.114+30092A>G		intron	N/A
	SMAD3-DT	ENST00000692307.3		n.91+30092A>G		intron	N/A
	SMAD3-DT	ENST00000701435.1		n.116+30092A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100653 AN: 151864 Hom.: 33489 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.663 AC: 100719 AN: 151982 Hom.: 33515 Cov.: 31 AF XY: 0.664 AC XY: 49290 AN XY: 74268

African (AFR) AF: 0.660 AC: 27320 AN: 41422

American (AMR) AF: 0.742 AC: 11343 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3342 AN: 5166

South Asian (SAS) AF: 0.549 AC: 2643 AN: 4816

European-Finnish (FIN) AF: 0.668 AC: 7056 AN: 10556

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.655 AC: 44537 AN: 67952

Other (OTH) AF: 0.669 AC: 1416 AN: 2116

Alfa AF: 0.663 Hom.: 12734

Bravo AF: 0.676

Asia WGS AF: 0.555 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		0.098

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7178347; hg19: chr15-67321386;