Variant 19-19279376-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_172231.4(SUGP1):c.1365C>T(p.Tyr455=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,604,516 control chromosomes in the GnomAD database, including 21,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2997 hom., cov: 33)

Exomes 𝑓: 0.15 ( 18411 hom. )

Consequence

SUGP1
NM_172231.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.222

Variant links:

Genes affected

SUGP1 (HGNC:18643): (SURP and G-patch domain containing 1) SF4 is a member of the SURP family of splicing factors.[supplied by OMIM, Sep 2003]

SUGP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 19-19279376-G-A is Benign according to our data. Variant chr19-19279376-G-A is described in ClinVar as [Benign]. Clinvar id is 1244931.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.222 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGP1	NM_172231.4 linkuse as main transcript	c.1365C>T	p.Tyr455=	synonymous_variant	10/14	ENST00000247001.10	NP_757386.2
SUGP1	XM_047439142.1 linkuse as main transcript	c.735C>T	p.Tyr245=	synonymous_variant	8/12		XP_047295098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGP1	ENST00000247001.10 linkuse as main transcript	c.1365C>T	p.Tyr455=	synonymous_variant	10/14	1	NM_172231.4	ENSP00000247001	P1	Q8IWZ8-1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27817

AN:

152074

Hom.:

2989

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0944

Gnomad FIN

AF:

0.0950

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.208

GnomAD3 exomes

AF:

0.138

AC:

33339

AN:

242044

Hom.:

2780

AF XY:

0.137

AC XY:

17971

AN XY:

131254

show subpopulations

Gnomad AFR exome

AF:

0.280

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.203

Gnomad EAS exome

AF:

0.000274

Gnomad SAS exome

AF:

0.0974

Gnomad FIN exome

AF:

0.0974

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.154

AC:

223931

AN:

1452324

Hom.:

18411

Cov.:

AF XY:

0.153

AC XY:

110840

AN XY:

722394

show subpopulations

Gnomad4 AFR exome

AF:

0.283

Gnomad4 AMR exome

AF:

0.109

Gnomad4 ASJ exome

AF:

0.201

Gnomad4 EAS exome

AF:

0.000328

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.0997

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.183

AC:

27864

AN:

152192

Hom.:

2997

Cov.:

AF XY:

0.178

AC XY:

13281

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.284

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.198

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0943

Gnomad4 FIN

AF:

0.0950

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.206

Alfa

AF:

0.170

Hom.:

4323

Bravo

AF:

0.191

Asia WGS

AF:

0.0560

AC:

197

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 02, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

6.6

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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.

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