rs2257073

Positions:

• chr7-151186200-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB10	NM_001142459.2	c.584+192G>A		intron_variant		ENST00000420175.3
ASB10	NM_001142460.1	c.584+192G>A		intron_variant
ASB10	NM_080871.4	c.539+192G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB10	ENST00000420175.3	c.584+192G>A		intron_variant		1	NM_001142459.2	P4
ASB10	ENST00000275838.5	c.584+192G>A		intron_variant		1
ASB10	ENST00000377867.7	c.539+192G>A		intron_variant		2		A1

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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.281

Alfa AF: 0.268 Hom.: 2749

Bravo AF: 0.259

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.60

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: rs2257073; hg19: chr7-150883287;