rs1861982

Variant names:

• chr2-53597926-G-A
• rs1861982
• ENST00000406053.5:c.*3+6901C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000406053.5(ASB3):​c.*3+6901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0669 in 152,206 control chromosomes in the GnomAD database, including 399 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 0.067 (399 hom., cov: 32)
• Consequence: ASB3 ENST00000406053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 1 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]

LOC105374600 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374600	XR_940087.4	n.1109+4297C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB3	ENST00000406053.5	c.*3+6901C>T		intron_variant	Intron 9 of 9	5		ENSP00000385137.1
ASB3	ENST00000482339.2	n.599+5459C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10163 AN: 152088 Hom.: 393 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0963

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0669 AC: 10189 AN: 152206 Hom.: 399 Cov.: 32 AF XY: 0.0697 AC XY: 5187 AN XY: 74426

African (AFR) AF: 0.0370 AC: 1535 AN: 41538

American (AMR) AF: 0.119 AC: 1825 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.124 AC: 599 AN: 4822

European-Finnish (FIN) AF: 0.0963 AC: 1019 AN: 10580

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0693 AC: 4716 AN: 68012

Other (OTH) AF: 0.0563 AC: 119 AN: 2112

Alfa AF: 0.0665 Hom.: 48

Bravo AF: 0.0680

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs1861982; hg19: chr2-53825063;