7-151187179-CAGAGAG-CAGAG

Variant names:

• chr7-151187179-CAG-C
• rs34383739
• NM_001142459.2:c.-51_-50delCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001142459.2(ASB10):​c.-51_-50delCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 1,116,648 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00067 (0 hom., cov: 22)
  • Exomes 𝑓: 0.073 (0 hom.)
• Consequence: ASB10 NM_001142459.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.639

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 -10 ACMG points.

• BP6: Variant 7-151187179-CAG-C is Benign according to our data. Variant chr7-151187179-CAG-C is described in ClinVar as [Benign]. Clinvar id is 402399.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.-51_-50delCT		5_prime_UTR_variant	Exon 1 of 6	ENST00000420175.3	NP_001135931.2
ASB10	NM_001142460.1	c.-51_-50delCT		5_prime_UTR_variant	Exon 1 of 5		NP_001135932.2
ASB10	NM_080871.4	c.271+271_271+272delCT		intron_variant	Intron 1 of 5		NP_543147.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175.3	c.-51_-50delCT		5_prime_UTR_variant	Exon 1 of 6	1	NM_001142459.2	ENSP00000391137.2
ASB10	ENST00000275838.5	c.-51_-50delCT		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000275838.1
ASB10	ENST00000377867.7	c.271+271_271+272delCT		intron_variant	Intron 1 of 5	2		ENSP00000367098.3
ASB10	ENST00000415615.1	n.*121+73_*121+74delCT		intron_variant	Intron 1 of 2	4		ENSP00000410871.1

Frequencies

GnomAD3 genomes AF: 0.000670 AC: 100 AN: 149144 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.000342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000467

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00321

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000671

Gnomad OTH AF: 0.000974

GnomAD4 exome AF: 0.0733 AC: 70914 AN: 967418 Hom.: 0 AF XY: 0.0784 AC XY: 37316 AN XY: 476098

Gnomad4 AFR exome AF: 0.0830

Gnomad4 AMR exome AF: 0.153

Gnomad4 ASJ exome AF: 0.0732

Gnomad4 EAS exome AF: 0.164

Gnomad4 SAS exome AF: 0.162

Gnomad4 FIN exome AF: 0.0827

Gnomad4 NFE exome AF: 0.0614

Gnomad4 OTH exome AF: 0.0785

GnomAD4 genome AF: 0.000670 AC: 100 AN: 149230 Hom.: 0 Cov.: 22 AF XY: 0.000701 AC XY: 51 AN XY: 72798

Gnomad4 AFR AF: 0.000341

Gnomad4 AMR AF: 0.000466

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00321

Gnomad4 NFE AF: 0.000671

Gnomad4 OTH AF: 0.000965

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34383739; hg19: chr7-150884266;