rs2209426

Variant names:

• chr9-17766317-G-A
• rs2209426
• NM_003026.5:c.187+4808G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-17766317-G-A
• chr9-17766317-G-C
• chr9-17766317-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003026.5(SH3GL2):​c.187+4808G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,194 control chromosomes in the GnomAD database, including 51,155 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 0.82 (51155 hom., cov: 33)
• Consequence: SH3GL2 NM_003026.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003026.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH3GL2	NM_003026.5	MANE Select	c.187+4808G>A		intron	N/A	NP_003017.1	Q99962

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH3GL2	ENST00000380607.5	TSL:1 MANE Select	c.187+4808G>A		intron	N/A	ENSP00000369981.4	Q99962
	SH3GL2	ENST00000955338.1		c.253+4808G>A		intron	N/A	ENSP00000625397.1
	SH3GL2	ENST00000917907.1		c.118+4808G>A		intron	N/A	ENSP00000587966.1

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124331 AN: 152076 Hom.: 51118 Cov.: 33

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.822

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.818 AC: 124419 AN: 152194 Hom.: 51155 Cov.: 33 AF XY: 0.813 AC XY: 60467 AN XY: 74394

African (AFR) AF: 0.809 AC: 33588 AN: 41514

American (AMR) AF: 0.706 AC: 10792 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3035 AN: 3468

East Asian (EAS) AF: 0.964 AC: 4984 AN: 5172

South Asian (SAS) AF: 0.757 AC: 3651 AN: 4826

European-Finnish (FIN) AF: 0.787 AC: 8333 AN: 10594

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57201 AN: 68016

Other (OTH) AF: 0.825 AC: 1745 AN: 2116

Alfa AF: 0.825 Hom.: 28290

Bravo AF: 0.815

Asia WGS AF: 0.840 AC: 2921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.61
PhyloP100		-0.022
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2209426; hg19: chr9-17766315;