rs13401104

Variant names:

• chr2-236196875-G-A
• rs13401104
• NM_212556.4:c.1102-490C>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.1102-490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,136 control chromosomes in the GnomAD database, including 3,261 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 0.20 (3261 hom., cov: 33)
• Consequence: ASB18 NM_212556.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB18	NM_212556.4	MANE Select	c.1102-490C>T		intron	N/A	NP_997721.2
	GBX2-AS1	NR_186035.1		n.229-16788G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB18	ENST00000409749.8	TSL:1 MANE Select	c.1102-490C>T		intron	N/A	ENSP00000386532.3
	ASB18	ENST00000645891.1		c.1015-490C>T		intron	N/A	ENSP00000496134.1
	ASB18	ENST00000447030.1	TSL:4	c.241-490C>T		intron	N/A	ENSP00000411434.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30532 AN: 152018 Hom.: 3245 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.201 AC: 30589 AN: 152136 Hom.: 3261 Cov.: 33 AF XY: 0.202 AC XY: 14996 AN XY: 74358

African (AFR) AF: 0.274 AC: 11384 AN: 41500

American (AMR) AF: 0.175 AC: 2677 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1068 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2007 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11451 AN: 67982

Other (OTH) AF: 0.168 AC: 356 AN: 2114

Alfa AF: 0.184 Hom.: 4322

Bravo AF: 0.200

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.68
PhyloP100		-1.2
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: rs13401104; hg19: chr2-237105518;