rs10490460

Variant names:

• chr2-53610295-C-T
• rs10490460
• ENST00000406053.5:c.1346-5380G>A

Variant summary

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

The ENST00000406053.5(ASB3):​c.1346-5380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0652 in 152,260 control chromosomes in the GnomAD database, including 385 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 0.065 (385 hom., cov: 33)
• Consequence: ASB3 ENST00000406053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 0 publications found

Genes affected

ASB3 (HGNC:16013): (ankyrin repeat and SOCS box containing 3) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. They contain ankyrin repeat sequence and SOCS box domain. The SOCS box serves to couple suppressor of cytokine signalling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB3	ENST00000406053.5	c.1346-5380G>A		intron_variant	Intron 8 of 9	5		ENSP00000385137.1

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9917 AN: 152142 Hom.: 381 Cov.: 33

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0652 AC: 9932 AN: 152260 Hom.: 385 Cov.: 33 AF XY: 0.0659 AC XY: 4906 AN XY: 74456

African (AFR) AF: 0.0970 AC: 4027 AN: 41528

American (AMR) AF: 0.0693 AC: 1060 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5184

South Asian (SAS) AF: 0.130 AC: 629 AN: 4824

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0476 AC: 3235 AN: 68024

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0545 Hom.: 367

Bravo AF: 0.0677

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10490460; hg19: chr2-53837432;