NM_003026.5:c.45+34155A>G

Variant names:

• chr9-17613442-A-G
• rs982019
• NM_003026.5:c.45+34155A>G

Variant summary

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

The NM_003026.5(SH3GL2):​c.45+34155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,122 control chromosomes in the GnomAD database, including 57,091 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 0.85 (57091 hom., cov: 31)
• Consequence: SH3GL2 NM_003026.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 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]

ENSG00000298472 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.968 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.45+34155A>G		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.45+34155A>G		intron	N/A	ENSP00000369981.4	Q99962
	SH3GL2	ENST00000955338.1		c.45+34155A>G		intron	N/A	ENSP00000625397.1
	SH3GL2	ENST00000917907.1		c.45+34155A>G		intron	N/A	ENSP00000587966.1

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128538 AN: 152004 Hom.: 57082 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.845 AC: 128584 AN: 152122 Hom.: 57091 Cov.: 31 AF XY: 0.852 AC XY: 63358 AN XY: 74362

African (AFR) AF: 0.540 AC: 22391 AN: 41438

American (AMR) AF: 0.925 AC: 14137 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3424 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4607 AN: 5176

South Asian (SAS) AF: 0.992 AC: 4778 AN: 4818

European-Finnish (FIN) AF: 0.978 AC: 10376 AN: 10614

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65802 AN: 68006

Other (OTH) AF: 0.891 AC: 1879 AN: 2108

Alfa AF: 0.880 Hom.: 7871

Bravo AF: 0.826

Asia WGS AF: 0.926 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		-1.6
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: rs982019; hg19: chr9-17613440;