chr2-53640050-G-T

Position:

• chr2-53640050-G-T

Variant summary

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

The ENST00000406053.5(ASB3):​c.1347-35135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 152,188 control chromosomes in the GnomAD database, including 479 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 0.075 (479 hom., cov: 32)
• Consequence: ASB3 ENST00000406053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB3	ENST00000406053.5	c.1347-35135C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11369 AN: 152070 Hom.: 478 Cov.: 32

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0981

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.0748 AC: 11377 AN: 152188 Hom.: 479 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74398

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0981

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0850

Gnomad4 FIN AF: 0.0530

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.0737 Hom.: 435

Bravo AF: 0.0803

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997644; hg19: chr2-53867187;