rs2257073

Variant names:

• chr7-151186200-C-T
• rs2257073
• NM_001142459.2:c.584+192G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001142459.2(ASB10):​c.584+192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,106 control chromosomes in the GnomAD database, including 5,132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (5132 hom., cov: 32)
• Consequence: ASB10 NM_001142459.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.162
• Publications: 1 publications found

Genes affected

ASB10 (HGNC:17185): (ankyrin repeat and SOCS box containing 10) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. The SOCS box serves to couple suppressor of cytokine signaling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2008]

ASB10 Gene-Disease associations (from GenCC):

• glaucoma 1, open angle, F

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 7-151186200-C-T is Benign according to our data. Variant chr7-151186200-C-T is described in ClinVar as Benign. ClinVar VariationId is 1248058.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142459.2. 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
	ASB10	NM_001142459.2	MANE Select	c.584+192G>A		intron	N/A	NP_001135931.2
	ASB10	NM_080871.4		c.539+192G>A		intron	N/A	NP_543147.2
	ASB10	NM_001142460.1		c.584+192G>A		intron	N/A	NP_001135932.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB10	ENST00000420175.3	TSL:1 MANE Select	c.584+192G>A		intron	N/A	ENSP00000391137.2
	ASB10	ENST00000275838.5	TSL:1	c.584+192G>A		intron	N/A	ENSP00000275838.1
	ASB10	ENST00000377867.7	TSL:2	c.539+192G>A		intron	N/A	ENSP00000367098.3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39027 AN: 151988 Hom.: 5130 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.257 AC: 39051 AN: 152106 Hom.: 5132 Cov.: 32 AF XY: 0.251 AC XY: 18670 AN XY: 74378

African (AFR) AF: 0.248 AC: 10296 AN: 41478

American (AMR) AF: 0.249 AC: 3807 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.102 AC: 528 AN: 5178

South Asian (SAS) AF: 0.205 AC: 990 AN: 4818

European-Finnish (FIN) AF: 0.221 AC: 2337 AN: 10594

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18931 AN: 67972

Other (OTH) AF: 0.281 AC: 592 AN: 2106

Alfa AF: 0.269 Hom.: 3050

Bravo AF: 0.259

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.60
PhyloP100		0.16
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: rs2257073; hg19: chr7-150883287;