rs7583622

chr2-53704053-G-Achr2-53704053-G-C

Variant summary

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

The NM_016115.5(ASB3):c.981-3525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 151,974 control chromosomes in the GnomAD database, including 4,101 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 0.23 (4101 hom., cov: 32)
• Consequence: ASB3 NM_016115.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB3	NM_016115.5	c.981-3525C>T		intron_variant		ENST00000263634.8
GPR75-ASB3	NM_001164165.2	c.1095-3525C>T		intron_variant
ASB3	NM_001201965.2	c.762-3525C>T		intron_variant
ASB3	NM_145863.3	c.762-3525C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB3	ENST00000263634.8	c.981-3525C>T		intron_variant		1	NM_016115.5	P1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34475 AN: 151856 Hom.: 4095 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.227 AC: 34509 AN: 151974 Hom.: 4101 Cov.: 32 AF XY: 0.234 AC XY: 17351 AN XY: 74262

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.218

Alfa AF: 0.203 Hom.: 5526

Bravo AF: 0.223

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.0
Dann	Benign	0.62

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: rs7583622; hg19: chr2-53931190;