Variant 1-172532477-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_016227.4(SUCO):c.5G>C(p.Arg2Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,611,898 control chromosomes in the GnomAD database, including 54 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 0.0035 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0022 ( 43 hom. )

Consequence

SUCO
NM_016227.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.20

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=0.0030939877).

BP6

Variant 1-172532477-G-C is Benign according to our data. Variant chr1-172532477-G-C is described in ClinVar as [Benign]. Clinvar id is 3033584.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-172532477-G-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00349 (531/152330) while in subpopulation EAS AF= 0.0498 (258/5180). AF 95% confidence interval is 0.0448. There are 11 homozygotes in gnomad4. There are 339 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCO	NM_016227.4 linkuse as main transcript	c.5G>C	p.Arg2Thr	missense_variant	1/23		NP_057311.3	Q9UBS9-2A0A024R929

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCO	ENST00000367723.8 linkuse as main transcript	c.5G>C	p.Arg2Thr	missense_variant	1/23	1		ENSP00000356696.4		Q9UBS9-2

Frequencies

GnomAD3 genomes

AF:

0.00349

AC:

531

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000482

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000392

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.0497

Gnomad SAS

AF:

0.00476

Gnomad FIN

AF:

0.0174

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000705

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00644

AC:

1568

AN:

243430

Hom.:

AF XY:

0.00607

AC XY:

803

AN XY:

132224

show subpopulations

Gnomad AFR exome

AF:

0.000134

Gnomad AMR exome

AF:

0.0000880

Gnomad ASJ exome

AF:

0.00132

Gnomad EAS exome

AF:

0.0616

Gnomad SAS exome

AF:

0.00123

Gnomad FIN exome

AF:

0.0144

Gnomad NFE exome

AF:

0.000715

Gnomad OTH exome

AF:

0.00370

GnomAD4 exome

AF:

0.00218

AC:

3176

AN:

1459568

Hom.:

Cov.:

AF XY:

0.00216

AC XY:

1569

AN XY:

725942

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.0000902

Gnomad4 ASJ exome

AF:

0.000810

Gnomad4 EAS exome

AF:

0.0440

Gnomad4 SAS exome

AF:

0.00154

Gnomad4 FIN exome

AF:

0.0137

Gnomad4 NFE exome

AF:

0.000336

Gnomad4 OTH exome

AF:

0.00269

GnomAD4 genome

AF:

0.00349

AC:

531

AN:

152330

Hom.:

Cov.:

AF XY:

0.00455

AC XY:

339

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0000481

Gnomad4 AMR

AF:

0.000392

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.0498

Gnomad4 SAS

AF:

0.00476

Gnomad4 FIN

AF:

0.0174

Gnomad4 NFE

AF:

0.000706

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00144

Hom.:

Bravo

AF:

0.00266

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000487

AC:

ExAC

AF:

0.00608

AC:

735

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.00104

EpiControl

AF:

0.000772

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

Jan 27, 2020

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

-0.47

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.86

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.55

FATHMM_MKL

Benign

0.37

LIST_S2

Benign

0.29

.;T

MetaRNN

Benign

0.0031

T;T

MetaSVM

Benign

-0.99

PROVEAN

Benign

0.090

N;.

REVEL

Benign

0.047

Sift

Pathogenic

0.0

D;.

Vest4

0.32

MVP

0.40

ClinPred

0.12

GERP RS

2.5

gMVP

0.018

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