Variant 9-17786430-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_003026.5(SH3GL2):c.237C>T(p.Gly79=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00238 in 1,613,322 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0023 ( 24 hom. )

Consequence

SH3GL2
NM_003026.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.81

Variant links:

Genes affected

SH3GL2 (HGNC:10831): (SH3 domain containing GRB2 like 2, endophilin A1) Enables identical protein binding activity. Involved in negative regulation of blood-brain barrier permeability; negative regulation of gene expression; and negative regulation of protein phosphorylation. Located in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SH3GL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 9-17786430-C-T is Benign according to our data. Variant chr9-17786430-C-T is described in ClinVar as [Benign]. Clinvar id is 708102.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.81 with no splicing effect.

BS2

High AC in GnomAd4 at 434 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SH3GL2	NM_003026.5 linkuse as main transcript	c.237C>T	p.Gly79=	synonymous_variant	4/9	ENST00000380607.5	NP_003017.1
SH3GL2	XM_011518005.4 linkuse as main transcript	c.339C>T	p.Gly113=	synonymous_variant	4/9		XP_011516307.1
SH3GL2	XM_047423730.1 linkuse as main transcript	c.132C>T	p.Gly44=	synonymous_variant	4/9		XP_047279686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3GL2	ENST00000380607.5 linkuse as main transcript	c.237C>T	p.Gly79=	synonymous_variant	4/9	1	NM_003026.5	ENSP00000369981	P1

Frequencies

GnomAD3 genomes

AF:

0.00285

AC:

434

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000327

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0133

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00369

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00292

AC:

730

AN:

250326

Hom.:

AF XY:

0.00307

AC XY:

416

AN XY:

135296

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.000175

Gnomad ASJ exome

AF:

0.00518

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00222

Gnomad FIN exome

AF:

0.0109

Gnomad NFE exome

AF:

0.00313

Gnomad OTH exome

AF:

0.00197

GnomAD4 exome

AF:

0.00233

AC:

3403

AN:

1461054

Hom.:

Cov.:

AF XY:

0.00240

AC XY:

1747

AN XY:

726860

show subpopulations

Gnomad4 AFR exome

AF:

0.000240

Gnomad4 AMR exome

AF:

0.000202

Gnomad4 ASJ exome

AF:

0.00517

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00217

Gnomad4 FIN exome

AF:

0.00985

Gnomad4 NFE exome

AF:

0.00220

Gnomad4 OTH exome

AF:

0.00152

GnomAD4 genome

AF:

0.00285

AC:

434

AN:

152268

Hom.:

Cov.:

AF XY:

0.00326

AC XY:

243

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0133

Gnomad4 NFE

AF:

0.00369

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00357

Hom.:

Bravo

AF:

0.00147

EpiCase

AF:

0.00196

EpiControl

AF:

0.00243

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

7.4

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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