18-48932662-T-C

Variant names:

• chr18-48932662-T-C
• rs4464148
• NM_005904.4:c.742+9819A>G

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+9819A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,060 control chromosomes in the GnomAD database, including 4,959 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 0.24 (4959 hom., cov: 32)
• Consequence: SMAD7 NM_005904.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 72 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD7	NM_005904.4	MANE Select	c.742+9819A>G		intron	N/A	NP_005895.1
	SMAD7	NM_001190821.2		c.739+9819A>G		intron	N/A	NP_001177750.1
	SMAD7	NM_001190823.2		c.178+9819A>G		intron	N/A	NP_001177752.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAD7	ENST00000262158.8	TSL:1 MANE Select	c.742+9819A>G		intron	N/A	ENSP00000262158.2
	SMAD7	ENST00000589634.1	TSL:4	c.739+9819A>G		intron	N/A	ENSP00000467621.1
	SMAD7	ENST00000591805.5	TSL:2	c.97+9819A>G		intron	N/A	ENSP00000466902.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37096 AN: 151942 Hom.: 4956 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.244 AC: 37105 AN: 152060 Hom.: 4959 Cov.: 32 AF XY: 0.237 AC XY: 17651 AN XY: 74340

African (AFR) AF: 0.172 AC: 7125 AN: 41442

American (AMR) AF: 0.236 AC: 3606 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1487 AN: 3472

East Asian (EAS) AF: 0.0609 AC: 316 AN: 5186

South Asian (SAS) AF: 0.0827 AC: 398 AN: 4814

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20645 AN: 67980

Other (OTH) AF: 0.287 AC: 603 AN: 2104

Alfa AF: 0.285 Hom.: 28700

Bravo AF: 0.242

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.50
PhyloP100		-0.19
Mutation Taster		=100/0	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: rs4464148; hg19: chr18-46459032;