Variant 16-30704198-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_006662.3(SRCAP):c.189C>G(p.Pro63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00583 in 1,614,168 control chromosomes in the GnomAD database, including 200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 98 hom., cov: 32)

Exomes 𝑓: 0.0041 ( 102 hom. )

Consequence

SRCAP
NM_006662.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.261

Variant links:

Genes affected

SRCAP (HGNC:16974): (Snf2 related CREBBP activator protein) This gene encodes the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex. The encoded protein is an ATPase that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. It can function as a transcriptional activator in Notch-mediated, CREB-mediated and steroid receptor-mediated transcription. Mutations in this gene cause Floating-Harbor syndrome, a rare disorder characterized by short stature, language deficits and dysmorphic facial features. [provided by RefSeq, Feb 2012]

SRCAP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 16-30704198-C-G is Benign according to our data. Variant chr16-30704198-C-G is described in ClinVar as [Benign]. Clinvar id is 160033.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.261 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRCAP	NM_006662.3 linkuse as main transcript	c.189C>G	p.Pro63=	synonymous_variant	4/34	ENST00000262518.9	NP_006653.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRCAP	ENST00000262518.9 linkuse as main transcript	c.189C>G	p.Pro63=	synonymous_variant	4/34	2	NM_006662.3	ENSP00000262518	P1	Q6ZRS2-1
SRCAP	ENST00000411466.7 linkuse as main transcript	c.189C>G	p.Pro63=	synonymous_variant	4/34	3		ENSP00000405186	P1	Q6ZRS2-1
SRCAP	ENST00000706321.1 linkuse as main transcript	c.189C>G	p.Pro63=	synonymous_variant	4/34			ENSP00000516346	P1	Q6ZRS2-1

Frequencies

GnomAD3 genomes

AF:

0.0228

AC:

3465

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0710

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0125

Gnomad ASJ

AF:

0.0360

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00237

Gnomad OTH

AF:

0.0186

GnomAD3 exomes

AF:

0.00795

AC:

1984

AN:

249552

Hom.:

AF XY:

0.00662

AC XY:

896

AN XY:

135400

show subpopulations

Gnomad AFR exome

AF:

0.0730

Gnomad AMR exome

AF:

0.00460

Gnomad ASJ exome

AF:

0.0354

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000556

Gnomad FIN exome

AF:

0.000557

Gnomad NFE exome

AF:

0.00238

Gnomad OTH exome

AF:

0.00627

GnomAD4 exome

AF:

0.00406

AC:

5939

AN:

1461890

Hom.:

102

Cov.:

AF XY:

0.00379

AC XY:

2759

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0734

Gnomad4 AMR exome

AF:

0.00525

Gnomad4 ASJ exome

AF:

0.0345

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000603

Gnomad4 FIN exome

AF:

0.000824

Gnomad4 NFE exome

AF:

0.00155

Gnomad4 OTH exome

AF:

0.00811

GnomAD4 genome

AF:

0.0228

AC:

3473

AN:

152278

Hom.:

Cov.:

AF XY:

0.0219

AC XY:

1631

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0710

Gnomad4 AMR

AF:

0.0125

Gnomad4 ASJ

AF:

0.0360

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00237

Gnomad4 OTH

AF:

0.0184

Alfa

AF:

0.00628

Hom.:

Bravo

AF:

0.0259

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.00229

EpiControl

AF:

0.00296

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Feb 08, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

6.3

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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