rs9325002

chr5-146046685-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152550.4(SH3RF2):c.1060-1087T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,098 control chromosomes in the GnomAD database, including 7,700 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 0.28 (7700 hom., cov: 32)
• Consequence: SH3RF2 NM_152550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

Genes affected

SH3RF2 (HGNC:26299): (SH3 domain containing ring finger 2) Enables protein phosphatase 1 binding activity and ubiquitin protein ligase activity. Involved in several processes, including positive regulation of JNK cascade; protein autoubiquitination; and regulation of cellular protein metabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC107986458 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SH3RF2	NM_152550.4	c.1060-1087T>C		intron_variant		ENST00000359120.9
LOC107986458	XR_001742913.2	n.285+20489A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH3RF2	ENST00000359120.9	c.1060-1087T>C		intron_variant		1	NM_152550.4	P1
SH3RF2	ENST00000511217.1	c.1060-1087T>C		intron_variant		1		P1
SH3RF2	ENST00000509286.1	n.187-1087T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42975 AN: 151982 Hom.: 7692 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 42995 AN: 152098 Hom.: 7700 Cov.: 32 AF XY: 0.281 AC XY: 20914 AN XY: 74352

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.267

Alfa AF: 0.336 Hom.: 1249

Bravo AF: 0.271

Asia WGS AF: 0.231 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs9325002; hg19: chr5-145426248;