18-48934533-C-G

Variant names:

• chr18-48934533-C-G
• rs2337106
• NM_005904.4:c.742+7948G>C

Variant summary

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

The NM_005904.4(SMAD7):​c.742+7948G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,806 control chromosomes in the GnomAD database, including 32,597 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 0.63 (32597 hom., cov: 31)
• Consequence: SMAD7 NM_005904.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 19 publications found

Genes affected

SMAD7 (HGNC:6773): (SMAD family member 7) The protein encoded by this gene is a nuclear protein that binds the E3 ubiquitin ligase SMURF2. Upon binding, this complex translocates to the cytoplasm, where it interacts with TGF-beta receptor type-1 (TGFBR1), leading to the degradation of both the encoded protein and TGFBR1. Expression of this gene is induced by TGFBR1. Variations in this gene are a cause of susceptibility to colorectal cancer type 3 (CRCS3). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

SMAD7 Gene-Disease associations (from GenCC):

• colorectal cancer, susceptibility to, 3

  Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia
• congenital heart disease

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005904.4. 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
	SMAD7	NM_005904.4	MANE Select	c.742+7948G>C		intron	N/A	NP_005895.1	O15105-1
	SMAD7	NM_001190821.2		c.739+7948G>C		intron	N/A	NP_001177750.1	O15105-3
	SMAD7	NM_001190823.2		c.178+7948G>C		intron	N/A	NP_001177752.1	B3KYA8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD7	ENST00000262158.8	TSL:1 MANE Select	c.742+7948G>C		intron	N/A	ENSP00000262158.2	O15105-1
	SMAD7	ENST00000589634.1	TSL:4	c.739+7948G>C		intron	N/A	ENSP00000467621.1	O15105-3
	SMAD7	ENST00000911789.1		c.668-12623G>C		intron	N/A	ENSP00000581848.1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95799 AN: 151688 Hom.: 32535 Cov.: 31

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.632 AC: 95915 AN: 151806 Hom.: 32597 Cov.: 31 AF XY: 0.628 AC XY: 46525 AN XY: 74116

African (AFR) AF: 0.903 AC: 37431 AN: 41460

American (AMR) AF: 0.524 AC: 7993 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2664 AN: 5166

South Asian (SAS) AF: 0.575 AC: 2770 AN: 4816

European-Finnish (FIN) AF: 0.524 AC: 5460 AN: 10424

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35515 AN: 67900

Other (OTH) AF: 0.632 AC: 1330 AN: 2104

Alfa AF: 0.400 Hom.: 924

Bravo AF: 0.643

Asia WGS AF: 0.623 AC: 2165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.39
DANN	Benign	0.68
PhyloP100		0.015
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2337106; hg19: chr18-46460903;