ENST00000367723.8:c.350T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000367723.8(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. 11/14 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
ENST00000367723.8 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.02

Publications

14 publications found

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 Gene-Disease associations (from GenCC):

osteogenesis imperfecta
Inheritance: AR Classification: MODERATE Submitted by: PanelApp Australia
temporal lobe epilepsy
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

SUCO links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000367723.8, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000367723.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SUCO	NM_014283.5	MANE Select	c.-236T>C		5_prime_UTR	Exon 1 of 24	NP_055098.1	Q9UBS9-1
SUCO	NM_016227.4		c.350T>C	p.Leu117Pro	missense	Exon 2 of 23	NP_057311.3	Q9UBS9-2
SUCO	NM_001282750.2		c.-236T>C		5_prime_UTR	Exon 1 of 23	NP_001269679.1	B4DYM4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SUCO	ENST00000367723.8	TSL:1	c.350T>C	p.Leu117Pro	missense	Exon 2 of 23	ENSP00000356696.4	Q9UBS9-2
SUCO	ENST00000263688.4	TSL:1 MANE Select	c.-236T>C		5_prime_UTR	Exon 1 of 24	ENSP00000263688.3	Q9UBS9-1
SUCO	ENST00000616058.4	TSL:1	c.-1765T>C		5_prime_UTR	Exon 1 of 22	ENSP00000479061.1	A0A087WV04

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

GnomAD2 exomes

AF:

0.270

AC:

31088

AN:

115266

AF XY:

0.276

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 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

African (AFR)

AF:

0.561

AC:

16817

AN:

29960

American (AMR)

AF:

0.220

AC:

7018

AN:

31914

Ashkenazi Jewish (ASJ)

AF:

0.325

AC:

7489

AN:

23030

East Asian (EAS)

AF:

0.197

AC:

6848

AN:

34820

South Asian (SAS)

AF:

0.391

AC:

29473

AN:

75468

European-Finnish (FIN)

AF:

0.187

AC:

7614

AN:

40804

Middle Eastern (MID)

AF:

0.387

AC:

1528

AN:

3944

European-Non Finnish (NFE)

AF:

0.244

AC:

258560

AN:

1061626

Other (OTH)

AF:

0.284

AC:

15910

AN:

56068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

14906

29812

44718

59624

74530

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9234

18468

27702

36936

46170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.335

AC:

50951

AN:

151920

Hom.:

10044

Cov.:

AF XY:

0.332

AC XY:

24674

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.554

AC:

22957

AN:

41468

American (AMR)

AF:

0.273

AC:

4174

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

1200

AN:

3470

East Asian (EAS)

AF:

0.189

AC:

969

AN:

5132

South Asian (SAS)

AF:

0.390

AC:

1879

AN:

4814

European-Finnish (FIN)

AF:

0.200

AC:

2111

AN:

10580

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.244

AC:

16558

AN:

67870

Other (OTH)

AF:

0.336

AC:

706

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1645

3290

4935

6580

8225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.274

Hom.:

1233

Bravo

AF:

0.348

Asia WGS

AF:

0.319

AC:

1111

AN:

3476

ClinVar

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

SUCO-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.56

Eigen

Benign

-0.89

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0096

LIST_S2

Benign

0.21

MetaRNN

Benign

0.000016

MetaSVM

Benign

-0.98

PhyloP100

-1.0

REVEL

Benign

0.012

Sift4G

Benign

0.17

PromoterAI

0.041

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.4

gMVP

0.053

Mutation Taster

=296/4

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over