rs5959087

Variant names:

• chrX-81235960-G-A
• rs5959087
• NM_003022.3:c.45+33715G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-81235960-G-A
• chrX-81235960-G-C

Variant summary

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

The NM_003022.3(SH3BGRL):​c.45+33715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 110,880 control chromosomes in the GnomAD database, including 1,688 homozygotes. There are 6,300 hemizygotes in GnomAD. 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 0.19 (1688 hom., 6300 hem., cov: 22)
• Consequence: SH3BGRL NM_003022.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 1 publications found

Genes affected

SH3BGRL (HGNC:10823): (SH3 domain binding glutamate rich protein like) Predicted to enable SH3 domain binding activity. Located in extracellular exosome. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003022.3. 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
	SH3BGRL	NM_003022.3	MANE Select	c.45+33715G>A		intron	N/A	NP_003013.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH3BGRL	ENST00000373212.6	TSL:1 MANE Select	c.45+33715G>A		intron	N/A	ENSP00000362308.5
	SH3BGRL	ENST00000481106.5	TSL:1	n.258+33384G>A		intron	N/A
	SH3BGRL	ENST00000963205.1		c.45+33715G>A		intron	N/A	ENSP00000633264.1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 20573 AN: 110825 Hom.: 1690 Cov.: 22

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0850

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.186 AC: 20589 AN: 110880 Hom.: 1688 Cov.: 22 AF XY: 0.190 AC XY: 6300 AN XY: 33122

African (AFR) AF: 0.0917 AC: 2808 AN: 30626

American (AMR) AF: 0.179 AC: 1875 AN: 10484

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 456 AN: 2636

East Asian (EAS) AF: 0.690 AC: 2368 AN: 3434

South Asian (SAS) AF: 0.414 AC: 1072 AN: 2587

European-Finnish (FIN) AF: 0.214 AC: 1254 AN: 5851

Middle Eastern (MID) AF: 0.211 AC: 45 AN: 213

European-Non Finnish (NFE) AF: 0.196 AC: 10357 AN: 52851

Other (OTH) AF: 0.195 AC: 296 AN: 1516

Alfa AF: 0.202 Hom.: 6738

Bravo AF: 0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.79
PhyloP100		0.27
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: rs5959087; hg19: chrX-80491459;