rs2278768

chr2-238446920-A-G

Variant summary

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

The NM_001040445.3(ASB1):c.*409A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 180,514 control chromosomes in the GnomAD database, including 3,823 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 0.16 (3734 hom., cov: 32)
  • Exomes 𝑓: 0.056 (89 hom.)
• Consequence: ASB1 NM_001040445.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB1	NM_001040445.3	c.*409A>G		3_prime_UTR_variant	5/5	ENST00000264607.9
ASB1	NM_001330196.2	c.*409A>G		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB1	ENST00000264607.9	c.*409A>G		3_prime_UTR_variant	5/5	1	NM_001040445.3	P1
ASB1	ENST00000481566.1	n.272+265A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24129 AN: 151992 Hom.: 3720 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.137

GnomAD4 exome AF: 0.0564 AC: 1601 AN: 28404 Hom.: 89 Cov.: 0 AF XY: 0.0562 AC XY: 843 AN XY: 14996

Gnomad4 AFR exome AF: 0.394

Gnomad4 AMR exome AF: 0.0858

Gnomad4 ASJ exome AF: 0.0243

Gnomad4 EAS exome AF: 0.113

Gnomad4 SAS exome AF: 0.0903

Gnomad4 FIN exome AF: 0.0740

Gnomad4 NFE exome AF: 0.0353

Gnomad4 OTH exome AF: 0.0733

GnomAD4 genome AF: 0.159 AC: 24184 AN: 152110 Hom.: 3734 Cov.: 32 AF XY: 0.161 AC XY: 11938 AN XY: 74364

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0661 Hom.: 795

Bravo AF: 0.169

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2278768; hg19: chr2-239355561;