2-53729843-C-A

Variant names:

• chr2-53729843-C-A
• rs6714424
• NM_016115.5:c.356-273G>T

Variant summary

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

The NM_016115.5(ASB3):​c.356-273G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,112 control chromosomes in the GnomAD database, including 2,336 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 0.17 (2336 hom., cov: 32)
• Consequence: ASB3 NM_016115.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 4 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]

GPR75-ASB3 (HGNC:40043): (GPR75-ASB3 readthrough) This locus represents naturally occurring read-through transcription between the neighboring GPR75 (G protein-coupled receptor 75) and ASB3 (ankyrin repeat and SOCS box containing 3) on chromosome 2. The transcript includes exons from both GPR75 and ASB3 and translation initiates in the 5' non-coding exon of GPR75. The resulting protein has a novel N-terminus but is otherwise identical to that encoded by ASB3.[provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB3	NM_016115.5	c.356-273G>T		intron_variant	Intron 3 of 9	ENST00000263634.8	NP_057199.1
GPR75-ASB3	NM_001164165.2	c.470-273G>T		intron_variant	Intron 3 of 9		NP_001157637.1
ASB3	NM_001201965.2	c.137-273G>T		intron_variant	Intron 2 of 8		NP_001188894.1
ASB3	NM_145863.3	c.137-273G>T		intron_variant	Intron 2 of 8		NP_665862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB3	ENST00000263634.8	c.356-273G>T		intron_variant	Intron 3 of 9	1	NM_016115.5	ENSP00000263634.2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25552 AN: 151994 Hom.: 2322 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.168 AC: 25605 AN: 152112 Hom.: 2336 Cov.: 32 AF XY: 0.167 AC XY: 12438 AN XY: 74380

African (AFR) AF: 0.247 AC: 10253 AN: 41486

American (AMR) AF: 0.170 AC: 2595 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3472

East Asian (EAS) AF: 0.180 AC: 932 AN: 5172

South Asian (SAS) AF: 0.106 AC: 513 AN: 4822

European-Finnish (FIN) AF: 0.151 AC: 1595 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8777 AN: 67974

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.108 Hom.: 247

Bravo AF: 0.174

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.30
PhyloP100		0.030
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs6714424; hg19: chr2-53956980;