Variant chr1-172533200-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_016227.4(SUCO):c.350T>C(p.Leu117Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,509,554 control chromosomes in the GnomAD database, including 58,598 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.34 ( 10044 hom., cov: 33)

Exomes 𝑓: 0.26 ( 48554 hom. )

Consequence

SUCO
NM_016227.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.02

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:

SUCO (HGNC:):

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=1.5810832E-5).

BP6

Variant 1-172533200-T-C is Benign according to our data. Variant chr1-172533200-T-C is described in ClinVar as [Benign]. Clinvar id is 3059036.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCO	NM_014283.5 linkuse as main transcript	c.-236T>C		5_prime_UTR_variant	1/24	ENST00000263688.4	NP_055098.1	Q9UBS9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SUCO	ENST00000367723.8 linkuse as main transcript	c.350T>C	p.Leu117Pro	missense_variant	2/23	1		ENSP00000356696.4	Q9UBS9-2
SUCO	ENST00000263688 linkuse as main transcript	c.-236T>C		5_prime_UTR_variant	1/24	1	NM_014283.5	ENSP00000263688.3	Q9UBS9-1
SUCO	ENST00000616058.4 linkuse as main transcript	c.-1765T>C		5_prime_UTR_variant	1/22	1		ENSP00000479061.1	A0A087WV04
SUCO	ENST00000610051 linkuse as main transcript	c.-236T>C		5_prime_UTR_variant	1/23	2		ENSP00000476704.1	B4DYM4

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50875

AN:

151810

Hom.:

10011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.332

GnomAD3 exomes

AF:

0.270

AC:

31088

AN:

115266

Hom.:

4828

AF XY:

0.276

AC XY:

17395

AN XY:

63018

show subpopulations

Gnomad AFR exome

AF:

0.545

Gnomad AMR exome

AF:

0.216

Gnomad ASJ exome

AF:

0.318

Gnomad EAS exome

AF:

0.176

Gnomad SAS exome

AF:

0.389

Gnomad FIN exome

AF:

0.185

Gnomad NFE exome

AF:

0.240

Gnomad OTH exome

AF:

0.278

GnomAD4 exome

AF:

0.259

AC:

351257

AN:

1357634

Hom.:

48554

Cov.:

AF XY:

0.262

AC XY:

174655

AN XY:

666534

show subpopulations

Gnomad4 AFR exome

AF:

0.561

Gnomad4 AMR exome

AF:

0.220

Gnomad4 ASJ exome

AF:

0.325

Gnomad4 EAS exome

AF:

0.197

Gnomad4 SAS exome

AF:

0.391

Gnomad4 FIN exome

AF:

0.187

Gnomad4 NFE exome

AF:

0.244

Gnomad4 OTH exome

AF:

0.284

GnomAD4 genome

AF:

0.335

AC:

50951

AN:

151920

Hom.:

10044

Cov.:

AF XY:

0.332

AC XY:

24674

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.554

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.189

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.244

Gnomad4 OTH

AF:

0.336

Alfa

AF:

0.274

Hom.:

1233

Bravo

AF:

0.348

TwinsUK

AF:

0.248

AC:

919

ALSPAC

AF:

0.241

AC:

928

ExAC

AF:

0.256

AC:

5332

Asia WGS

AF:

0.319

AC:

1111

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SUCO-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 31, 2019

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

DANN

Benign

0.56

Eigen

Benign

-0.89

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0096

LIST_S2

Benign

0.21

.;T

MetaRNN

Benign

0.000016

T;T

MetaSVM

Benign

-0.98

REVEL

Benign

0.012

Sift4G

Benign

0.17

T;T

Vest4

0.097

ClinPred

0.0060

GERP RS

-3.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.4

gMVP

0.053

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