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GeneBe

rs2224451

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003026.5(SH3GL2):​c.45+57469T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,230 control chromosomes in the GnomAD database, including 63,675 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.90 ( 63675 hom., cov: 32)

Consequence

SH3GL2
NM_003026.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.266
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SH3GL2NM_003026.5 linkuse as main transcriptc.45+57469T>A intron_variant ENST00000380607.5
SH3GL2XM_011518005.4 linkuse as main transcriptc.147+18541T>A intron_variant
SH3GL2XM_047423730.1 linkuse as main transcriptc.-61+29502T>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SH3GL2ENST00000380607.5 linkuse as main transcriptc.45+57469T>A intron_variant 1 NM_003026.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.904
AC:
137447
AN:
152112
Hom.:
63631
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.676
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.961
Gnomad ASJ
AF:
0.975
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.971
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.949
Gnomad NFE
AF:
0.996
Gnomad OTH
AF:
0.935
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.904
AC:
137549
AN:
152230
Hom.:
63675
Cov.:
32
AF XY:
0.907
AC XY:
67492
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.676
Gnomad4 AMR
AF:
0.961
Gnomad4 ASJ
AF:
0.975
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.971
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.996
Gnomad4 OTH
AF:
0.936
Alfa
AF:
0.947
Hom.:
8090
Bravo
AF:
0.891
Asia WGS
AF:
0.973
AC:
3383
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
1.1
DANN
Benign
0.69

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.

Other links and lift over

dbSNP: rs2224451; hg19: chr9-17636754; API