GeneBe

rs7034773

Positions:

Variant summary

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

The NM_003026.5(SH3GL2):​c.45+27752G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,184 control chromosomes in the GnomAD database, including 3,083 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 0.11 ( 3083 hom., cov: 32)

Consequence

SH3GL2
NM_003026.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.726
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
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SH3GL2NM_003026.5 linkuse as main transcriptc.45+27752G>A intron_variant ENST00000380607.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SH3GL2ENST00000380607.5 linkuse as main transcriptc.45+27752G>A intron_variant 1 NM_003026.5 P1
SH3GL2ENST00000467085.1 linkuse as main transcriptn.207-23315G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.110
AC:
16679
AN:
152066
Hom.:
3084
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.383
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0387
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00118
Gnomad OTH
AF:
0.0760
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.110
AC:
16706
AN:
152184
Hom.:
3083
Cov.:
32
AF XY:
0.104
AC XY:
7767
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.382
Gnomad4 AMR
AF:
0.0387
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.00166
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00118
Gnomad4 OTH
AF:
0.0752
Alfa
AF:
0.0359
Hom.:
105
Bravo
AF:
0.126
Asia WGS
AF:
0.0230
AC:
82
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
5.6
DANN
Benign
0.66

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: rs7034773; hg19: chr9-17607037; API