rs7162912

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000327367.9(SMAD3):​c.206+2610T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 151,992 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00011 ( 0 hom., cov: 30)

Consequence

SMAD3
ENST00000327367.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0750
Variant links:
Genes affected
SMAD3 (HGNC:6769): (SMAD family member 3) The SMAD family of proteins are a group of intracellular signal transducer proteins similar to the gene products of the Drosophila gene 'mothers against decapentaplegic' (Mad) and the C. elegans gene Sma. The SMAD3 protein functions in the transforming growth factor-beta signaling pathway, and transmits signals from the cell surface to the nucleus, regulating gene activity and cell proliferation. This protein forms a complex with other SMAD proteins and binds DNA, functioning both as a transcription factor and tumor suppressor. Mutations in this gene are associated with aneurysms-osteoarthritis syndrome and Loeys-Dietz Syndrome 3. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
High AC in GnomAd4 at 17 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SMAD3NM_005902.4 linkuse as main transcriptc.206+2610T>A intron_variant ENST00000327367.9 NP_005893.1
SMAD3NM_001407011.1 linkuse as main transcriptc.206+2610T>A intron_variant NP_001393940.1
SMAD3NM_001407012.1 linkuse as main transcriptc.206+2610T>A intron_variant NP_001393941.1
SMAD3NM_001407013.1 linkuse as main transcriptc.206+2610T>A intron_variant NP_001393942.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SMAD3ENST00000327367.9 linkuse as main transcriptc.206+2610T>A intron_variant 1 NM_005902.4 ENSP00000332973 P1P84022-1
SMAD3ENST00000559460.6 linkuse as main transcriptc.-110+5026T>A intron_variant 4 ENSP00000453082
SMAD3ENST00000560424.2 linkuse as main transcriptc.206+2610T>A intron_variant 3 ENSP00000455540
SMAD3ENST00000679624.1 linkuse as main transcriptc.-110+1057T>A intron_variant ENSP00000505445 P84022-3

Frequencies

GnomAD3 genomes
AF:
0.0000856
AC:
13
AN:
151870
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000315
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000112
AC:
17
AN:
151992
Hom.:
0
Cov.:
30
AF XY:
0.000148
AC XY:
11
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.000410
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.7
DANN
Benign
0.84
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7162912; hg19: chr15-67361308; API