chr7-151175959-A-G

Position:

• chr7-151175959-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001142459.2(ASB10):​c.*8T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,003,206 control chromosomes in the GnomAD database, including 78,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.46 (17471 hom., cov: 33)
  • Exomes 𝑓: 0.37 (60859 hom.)
• Consequence: ASB10 NM_001142459.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.340

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 7-151175959-A-G is Benign according to our data. Variant chr7-151175959-A-G is described in ClinVar as [Benign]. Clinvar id is 1221472.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.*8T>C		3_prime_UTR_variant	6/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4	c.*8T>C		3_prime_UTR_variant	6/6		NP_543147.2
ASB10	NM_001142460.1	c.*8T>C		3_prime_UTR_variant	5/5		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175	c.*8T>C		3_prime_UTR_variant	6/6	1	NM_001142459.2	ENSP00000391137.2
ASB10	ENST00000275838	c.*8T>C		3_prime_UTR_variant	5/5	1		ENSP00000275838.1
ASB10	ENST00000377867	c.*8T>C		3_prime_UTR_variant	6/6	2		ENSP00000367098.3

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69551 AN: 151948 Hom.: 17444 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.450

GnomAD4 exome AF: 0.373 AC: 317345 AN: 851140 Hom.: 60859 Cov.: 11 AF XY: 0.369 AC XY: 156909 AN XY: 424696

Gnomad4 AFR exome AF: 0.682

Gnomad4 AMR exome AF: 0.334

Gnomad4 ASJ exome AF: 0.419

Gnomad4 EAS exome AF: 0.338

Gnomad4 SAS exome AF: 0.291

Gnomad4 FIN exome AF: 0.410

Gnomad4 NFE exome AF: 0.369

Gnomad4 OTH exome AF: 0.394

GnomAD4 genome AF: 0.458 AC: 69625 AN: 152066 Hom.: 17471 Cov.: 33 AF XY: 0.454 AC XY: 33739 AN XY: 74334

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.449

Alfa AF: 0.387 Hom.: 13681

Bravo AF: 0.469

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.87
CADD	Benign	3.2
DANN	Benign	0.78

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: rs310597; hg19: chr7-150873046; COSMIC: COSV51995139; COSMIC: COSV51995139;