2-53597926-G-A

Position:

• chr2-53597926-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_940087.4(LOC105374600):​n.1109+4297C>T variant causes a intron, non coding transcript 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: LOC105374600 XR_940087.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

Genes affected

LOC105374600 (HGNC:):

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 -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/exons	MANE	UniProt
LOC105374600	XR_940087.4	n.1109+4297C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB3	ENST00000406053.5	c.*3+6901C>T		intron_variant		5
ASB3	ENST00000482339.2	n.599+5459C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0963

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0677 Hom.: 47

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861982; hg19: chr2-53825063;