rs13407662

Variant names:

• chr2-53555422-C-T
• rs13407662
• ENST00000406053.5:c.*4-21538G>A

Variant summary

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

The ENST00000406053.5(ASB3):​c.*4-21538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 152,310 control chromosomes in the GnomAD database, including 161 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 0.043 (161 hom., cov: 33)
• Consequence: ASB3 ENST00000406053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0521 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.*4-21538G>A		intron_variant	Intron 9 of 9	5		ENSP00000385137.1

Frequencies

GnomAD3 genomes AF: 0.0427 AC: 6502 AN: 152192 Hom.: 160 Cov.: 33

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0427 AC: 6504 AN: 152310 Hom.: 161 Cov.: 33 AF XY: 0.0406 AC XY: 3021 AN XY: 74480

African (AFR) AF: 0.0539 AC: 2242 AN: 41560

American (AMR) AF: 0.0361 AC: 553 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4828

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10618

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0459 AC: 3125 AN: 68028

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0462 Hom.: 494

Bravo AF: 0.0445

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs13407662; hg19: chr2-53782559;