rs13390159

Positions:

• chr2-236247906-G-A

Variant summary

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

The NM_212556.4(ASB18):​c.206-6504C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,116 control chromosomes in the GnomAD database, including 7,865 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 0.26 (7865 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ASB18 NM_212556.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

Genes affected

ASB18 (HGNC:19770): (ankyrin repeat and SOCS box containing 18) 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 a 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. [provided by RefSeq, Feb 2017]

GBX2-AS1 (HGNC:55714): (GBX2 and ASB18 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB18	NM_212556.4	c.206-6504C>T		intron_variant		ENST00000409749.8	NP_997721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB18	ENST00000409749.8	c.206-6504C>T		intron_variant		1	NM_212556.4	ENSP00000386532	P1
ASB18	ENST00000487961.1	n.3050C>T		non_coding_transcript_exon_variant	2/2	1
GBX2-AS1	ENST00000415226.1	n.224-11601G>A		intron_variant, non_coding_transcript_variant		4
ASB18	ENST00000430053.1	c.206-9950C>T		intron_variant		5		ENSP00000410021

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39780 AN: 151998 Hom.: 7852 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.248

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.262 AC: 39828 AN: 152116 Hom.: 7865 Cov.: 32 AF XY: 0.256 AC XY: 19027 AN XY: 74362

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.246

Alfa AF: 0.165 Hom.: 5799

Bravo AF: 0.277

Asia WGS AF: 0.135 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.45

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: rs13390159; hg19: chr2-237156549;