dbSNP rs2239816: SUCO:p.Ser11Pro (chr1-172532503-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_016227.4(SUCO):c.31T>C(p.Ser11Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,612,794 control chromosomes in the GnomAD database, including 50,697 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.23 ( 4333 hom., cov: 32)

Exomes 𝑓: 0.25 ( 46364 hom. )

Consequence

SUCO
NM_016227.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.72

Variant links:

Genes affected

SUCO (HGNC:1240): (SUN domain containing ossification factor) Predicted to be involved in positive regulation of collagen biosynthetic process; positive regulation of osteoblast differentiation; and regulation of bone remodeling. Predicted to be located in rough endoplasmic reticulum. Predicted to be active in cytoplasm and membrane. [provided by Alliance of Genome Resources, Apr 2022]

SUCO links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0033645928).

BP6

Variant 1-172532503-T-C is Benign according to our data. Variant chr1-172532503-T-C is described in ClinVar as [Benign]. Clinvar id is 3059072.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCO	NM_016227.4 link	c.31T>C	p.Ser11Pro	missense_variant	Exon 1 of 23		NP_057311.3	Q9UBS9-2A0A024R929

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUCO	ENST00000367723.8 link	c.31T>C	p.Ser11Pro	missense_variant	Exon 1 of 23	1		ENSP00000356696.4		Q9UBS9-2

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35615

AN:

152044

Hom.:

4325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.246

AC:

60309

AN:

244896

Hom.:

8012

AF XY:

0.255

AC XY:

33914

AN XY:

132976

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.200

Gnomad ASJ exome

AF:

0.328

Gnomad EAS exome

AF:

0.183

Gnomad SAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.193

Gnomad NFE exome

AF:

0.246

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.248

AC:

361639

AN:

1460632

Hom.:

46364

Cov.:

AF XY:

0.252

AC XY:

183201

AN XY:

726520

show subpopulations

Gnomad4 AFR exome

AF:

0.204

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.325

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.191

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.257

GnomAD4 genome

AF:

0.234

AC:

35637

AN:

152162

Hom.:

4333

Cov.:

AF XY:

0.234

AC XY:

17409

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.207

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.247

Hom.:

8335

Bravo

AF:

0.233

TwinsUK

AF:

0.247

AC:

917

ALSPAC

AF:

0.239

AC:

923

ESP6500AA

AF:

0.205

AC:

787

ESP6500EA

AF:

0.248

AC:

2051

ExAC

AF:

0.251

AC:

30274

Asia WGS

AF:

0.278

AC:

966

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SUCO-related disorder

Benign:1

Oct 31, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

0.73

DANN

Benign

0.57

Eigen

Benign

-0.85

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.018

LIST_S2

Benign

0.26

.;T

MetaRNN

Benign

0.0034

T;T

MetaSVM

Benign

-0.96

PROVEAN

Benign

-0.20

N;.

REVEL

Benign

0.0050

Sift

Pathogenic

0.0

D;.

Sift4G

Benign

0.35

T;T

Vest4

0.077

ClinPred

0.013

GERP RS

-1.3

gMVP

0.017

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over