7-151176521-A-G

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.1218+42T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 1,522,122 control chromosomes in the GnomAD database, including 114,667 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.46 (17334 hom., cov: 33)
  • Exomes 𝑓: 0.37 (97333 hom.)
• Consequence: ASB10 NM_001142459.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0560

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 7-151176521-A-G is Benign according to our data. Variant chr7-151176521-A-G is described in ClinVar as [Benign]. Clinvar id is 1244215.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB10	NM_001142459.2	c.1218+42T>C		intron_variant		ENST00000420175.3
ASB10	NM_001142460.1	c.1105-224T>C		intron_variant
ASB10	NM_080871.4	c.1173+42T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB10	ENST00000420175.3	c.1218+42T>C		intron_variant		1	NM_001142459.2	P4
ASB10	ENST00000275838.5	c.1105-224T>C		intron_variant		1
ASB10	ENST00000377867.7	c.1173+42T>C		intron_variant		2		A1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69335 AN: 151914 Hom.: 17307 Cov.: 33

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.450

GnomAD3 exomes AF: 0.369 AC: 55631 AN: 150632 Hom.: 11005 AF XY: 0.363 AC XY: 29037 AN XY: 79892

Gnomad AFR exome AF: 0.686

Gnomad AMR exome AF: 0.302

Gnomad ASJ exome AF: 0.411

Gnomad EAS exome AF: 0.337

Gnomad SAS exome AF: 0.290

Gnomad FIN exome AF: 0.413

Gnomad NFE exome AF: 0.371

Gnomad OTH exome AF: 0.377

GnomAD4 exome AF: 0.372 AC: 509964 AN: 1370090 Hom.: 97333 Cov.: 30 AF XY: 0.369 AC XY: 248772 AN XY: 673472

Gnomad4 AFR exome AF: 0.683

Gnomad4 AMR exome AF: 0.315

Gnomad4 ASJ exome AF: 0.416

Gnomad4 EAS exome AF: 0.340

Gnomad4 SAS exome AF: 0.293

Gnomad4 FIN exome AF: 0.412

Gnomad4 NFE exome AF: 0.368

Gnomad4 OTH exome AF: 0.391

GnomAD4 genome AF: 0.457 AC: 69409 AN: 152032 Hom.: 17334 Cov.: 33 AF XY: 0.453 AC XY: 33639 AN XY: 74336

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.449

Alfa AF: 0.420 Hom.: 2539

Bravo AF: 0.467

Asia WGS AF: 0.346 AC: 1205 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.8
Dann	Benign	0.50

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: rs310598; hg19: chr7-150873608; COSMIC: COSV52000830; COSMIC: COSV52000830;