rs2400207

Positions:

• chr5-146000534-A-G
• chr5-146000534-A-T

Variant summary

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

The NM_152550.4(SH3RF2):​c.648+207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,054 control chromosomes in the GnomAD database, including 24,763 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 0.56 (24763 hom., cov: 33)
• Consequence: SH3RF2 NM_152550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SH3RF2	NM_152550.4	c.648+207A>G		intron_variant		ENST00000359120.9
LOC107986458	XR_001742913.2	n.378-4110T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH3RF2	ENST00000359120.9	c.648+207A>G		intron_variant		1	NM_152550.4	P1
SH3RF2	ENST00000511217.1	c.648+207A>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85594 AN: 151938 Hom.: 24763 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.563 AC: 85627 AN: 152054 Hom.: 24763 Cov.: 33 AF XY: 0.571 AC XY: 42423 AN XY: 74310

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.630

Alfa AF: 0.564 Hom.: 3874

Bravo AF: 0.554

Asia WGS AF: 0.735 AC: 2548 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.28

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: rs2400207; hg19: chr5-145380097;