rs3808772

Variant names:

• chr9-17598289-C-T
• rs3808772
• NM_003026.5:c.45+19002C>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.45+19002C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,104 control chromosomes in the GnomAD database, including 39,917 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 0.72 (39917 hom., cov: 32)
• Consequence: SH3GL2 NM_003026.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3GL2	NM_003026.5	c.45+19002C>T		intron_variant	Intron 1 of 8	ENST00000380607.5	NP_003017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3GL2	ENST00000380607.5	c.45+19002C>T		intron_variant	Intron 1 of 8	1	NM_003026.5	ENSP00000369981.4
SH3GL2	ENST00000467085.1	n.206+19002C>T		intron_variant	Intron 1 of 1	5
ENSG00000298472	ENST00000755729.1	n.435+42946C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109766 AN: 151986 Hom.: 39882 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.722 AC: 109860 AN: 152104 Hom.: 39917 Cov.: 32 AF XY: 0.719 AC XY: 53451 AN XY: 74362

African (AFR) AF: 0.775 AC: 32186 AN: 41508

American (AMR) AF: 0.737 AC: 11258 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2481 AN: 3472

East Asian (EAS) AF: 0.530 AC: 2727 AN: 5144

South Asian (SAS) AF: 0.590 AC: 2844 AN: 4818

European-Finnish (FIN) AF: 0.714 AC: 7561 AN: 10584

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48378 AN: 67996

Other (OTH) AF: 0.736 AC: 1552 AN: 2110

Alfa AF: 0.714 Hom.: 129427

Bravo AF: 0.726

Asia WGS AF: 0.603 AC: 2095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		-0.35
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: rs3808772; hg19: chr9-17598287;