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GeneBe

rs10491262

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000511217.1(SH3RF2):c.*34-7608T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,330 control chromosomes in the GnomAD database, including 676 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 0.053 ( 676 hom., cov: 32)

Consequence

SH3RF2
ENST00000511217.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.158
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SH3RF2XM_006714757.2 linkuse as main transcriptc.*34-7608T>C intron_variant
SH3RF2XM_011537568.3 linkuse as main transcriptc.*34-7608T>C intron_variant
SH3RF2XM_017009136.2 linkuse as main transcriptc.*34-7608T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SH3RF2ENST00000511217.1 linkuse as main transcriptc.*34-7608T>C intron_variant 1 P1Q8TEC5-1

Frequencies

GnomAD3 genomes
AF:
0.0530
AC:
8062
AN:
152212
Hom.:
672
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0273
Gnomad ASJ
AF:
0.0245
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00745
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.00172
Gnomad OTH
AF:
0.0449
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0531
AC:
8083
AN:
152330
Hom.:
676
Cov.:
32
AF XY:
0.0518
AC XY:
3859
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.176
Gnomad4 AMR
AF:
0.0272
Gnomad4 ASJ
AF:
0.0245
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00746
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00170
Gnomad4 OTH
AF:
0.0444
Alfa
AF:
0.0452
Hom.:
59
Bravo
AF:
0.0604
Asia WGS
AF:
0.0150
AC:
54
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
8.1
Dann
Benign
0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10491262; hg19: chr5-145450415; API