rs3808747

Variant names:

• chr9-17626618-C-T
• rs3808747
• NM_003026.5:c.45+47331C>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+47331C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,104 control chromosomes in the GnomAD database, including 2,169 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 0.17 (2169 hom., cov: 32)
• Consequence: SH3GL2 NM_003026.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3GL2	NM_003026.5	c.45+47331C>T		intron_variant	Intron 1 of 8	ENST00000380607.5	NP_003017.1
SH3GL2	XM_011518005.4	c.147+8403C>T		intron_variant	Intron 1 of 8		XP_011516307.1
SH3GL2	XM_047423730.1	c.-61+19364C>T		intron_variant	Intron 1 of 8		XP_047279686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3GL2	ENST00000380607.5	c.45+47331C>T		intron_variant	Intron 1 of 8	1	NM_003026.5	ENSP00000369981.4
SH3GL2	ENST00000467085.1	n.207-3736C>T		intron_variant	Intron 1 of 1	5
ENSG00000298472	ENST00000755729.1	n.436-27444C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25122 AN: 151984 Hom.: 2166 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.165 AC: 25141 AN: 152104 Hom.: 2169 Cov.: 32 AF XY: 0.165 AC XY: 12285 AN XY: 74342

African (AFR) AF: 0.210 AC: 8693 AN: 41480

American (AMR) AF: 0.137 AC: 2098 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.141 AC: 726 AN: 5162

South Asian (SAS) AF: 0.170 AC: 820 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1468 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10098 AN: 68000

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.156 Hom.: 8382

Bravo AF: 0.166

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		-0.032
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: rs3808747; hg19: chr9-17626616;