rs1044561

Positions:

• chr2-238446677-C-A

Variant summary

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

The NM_001040445.3(ASB1):​c.*166C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 780,540 control chromosomes in the GnomAD database, including 4,834 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 0.14 (2605 hom., cov: 32)
  • Exomes 𝑓: 0.063 (2229 hom.)
• Consequence: ASB1 NM_001040445.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582

Genes affected

ASB1 (HGNC:16011): (ankyrin repeat and SOCS box containing 1) The protein encoded by this gene contains an 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, targeting them for ubiquitination and degradation. [provided by RefSeq, Aug 2016]

ASB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB1	NM_001040445.3	c.*166C>A		3_prime_UTR_variant	5/5	ENST00000264607.9	NP_001035535.1
ASB1	NM_001330196.2	c.*166C>A		3_prime_UTR_variant	4/4		NP_001317125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB1	ENST00000264607.9	c.*166C>A		3_prime_UTR_variant	5/5	1	NM_001040445.3	ENSP00000264607.4
ASB1	ENST00000481566.1	n.272+22C>A		intron_variant		5
ASB1	ENST00000438264.5	n.*846C>A		downstream_gene_variant		3		ENSP00000411773.1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20696 AN: 151934 Hom.: 2596 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0364

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.118

GnomAD4 exome AF: 0.0630 AC: 39614 AN: 628488 Hom.: 2229 Cov.: 8 AF XY: 0.0635 AC XY: 21062 AN XY: 331572

Gnomad4 AFR exome AF: 0.336

Gnomad4 AMR exome AF: 0.106

Gnomad4 ASJ exome AF: 0.0358

Gnomad4 EAS exome AF: 0.102

Gnomad4 SAS exome AF: 0.101

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.0385

Gnomad4 OTH exome AF: 0.0749

GnomAD4 genome AF: 0.136 AC: 20745 AN: 152052 Hom.: 2605 Cov.: 32 AF XY: 0.139 AC XY: 10321 AN XY: 74326

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0364

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0795 Hom.: 269

Bravo AF: 0.142

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1044561; hg19: chr2-239355318;