rs2015983

Variant names:

• chr2-236241523-A-C
• rs2015983
• NM_212556.4:c.206-121T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-236241523-A-C
• chr2-236241523-A-T

Variant summary

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

The NM_212556.4(ASB18):​c.206-121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 1,163,224 control chromosomes in the GnomAD database, including 357,981 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 0.76 (44162 hom., cov: 32)
  • Exomes 𝑓: 0.79 (313819 hom.)
• Consequence: ASB18 NM_212556.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 9 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_212556.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB18	NM_212556.4	MANE Select	c.206-121T>G		intron	N/A	NP_997721.2	Q6ZVZ8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB18	ENST00000409749.8	TSL:1 MANE Select	c.206-121T>G		intron	N/A	ENSP00000386532.3	Q6ZVZ8-1
	ASB18	ENST00000430053.1	TSL:5	c.206-3567T>G		intron	N/A	ENSP00000410021.1	C9JFL4
	GBX2-AS1	ENST00000415226.1	TSL:4	n.224-17984A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115208 AN: 151974 Hom.: 44132 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.783

GnomAD2 exomes AF: 0.801 AC: 127696 AN: 159386 AF XY: 0.803

Gnomad AFR exome AF: 0.653

Gnomad AMR exome AF: 0.831

Gnomad ASJ exome AF: 0.838

Gnomad EAS exome AF: 0.793

Gnomad FIN exome AF: 0.822

Gnomad NFE exome AF: 0.795

Gnomad OTH exome AF: 0.811

GnomAD4 exome AF: 0.787 AC: 795496 AN: 1011132 Hom.: 313819 Cov.: 13 AF XY: 0.789 AC XY: 407419 AN XY: 516204

African (AFR) AF: 0.641 AC: 15767 AN: 24582

American (AMR) AF: 0.825 AC: 29344 AN: 35570

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 19127 AN: 22752

East Asian (EAS) AF: 0.839 AC: 29004 AN: 34562

South Asian (SAS) AF: 0.819 AC: 59349 AN: 72424

European-Finnish (FIN) AF: 0.821 AC: 35764 AN: 43582

Middle Eastern (MID) AF: 0.804 AC: 3965 AN: 4930

European-Non Finnish (NFE) AF: 0.781 AC: 567616 AN: 727224

Other (OTH) AF: 0.781 AC: 35560 AN: 45506

GnomAD4 genome AF: 0.758 AC: 115287 AN: 152092 Hom.: 44162 Cov.: 32 AF XY: 0.764 AC XY: 56785 AN XY: 74342

African (AFR) AF: 0.652 AC: 27024 AN: 41466

American (AMR) AF: 0.805 AC: 12303 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3470

East Asian (EAS) AF: 0.797 AC: 4118 AN: 5168

South Asian (SAS) AF: 0.820 AC: 3949 AN: 4818

European-Finnish (FIN) AF: 0.821 AC: 8693 AN: 10586

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53583 AN: 67986

Other (OTH) AF: 0.786 AC: 1658 AN: 2110

Alfa AF: 0.782 Hom.: 25677

Bravo AF: 0.752

Asia WGS AF: 0.811 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.31
PhyloP100		-0.098
PromoterAI		0.020	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs2015983; hg19: chr2-237150166;