rs13390159

Variant names:

• chr2-236247906-G-A
• rs13390159
• ENST00000487961.1:n.3050C>T

Variant summary

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

The ENST00000487961.1(ASB18):​n.3050C>T variant causes a non coding transcript exon 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 ENST00000487961.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487961.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB18	NM_212556.4	MANE Select	c.206-6504C>T		intron	N/A	NP_997721.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB18	ENST00000487961.1	TSL:1	n.3050C>T		non_coding_transcript_exon	Exon 2 of 2
	ASB18	ENST00000409749.8	TSL:1 MANE Select	c.206-6504C>T		intron	N/A	ENSP00000386532.3
	ASB18	ENST00000430053.1	TSL:5	c.206-9950C>T		intron	N/A	ENSP00000410021.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.561 AC: 23241 AN: 41460

American (AMR) AF: 0.170 AC: 2598 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5184

South Asian (SAS) AF: 0.195 AC: 940 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1339 AN: 10590

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10165 AN: 67986

Other (OTH) AF: 0.246 AC: 521 AN: 2116

Alfa AF: 0.180 Hom.: 15474

Bravo AF: 0.277

Asia WGS AF: 0.135 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.45
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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: rs13390159; hg19: chr2-237156549;