chr7-151187179-C-CAG

Position:

• chr7-151187179-C-CAG

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_001142459.2(ASB10):​c.-51_-50dupCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,483,822 control chromosomes in the GnomAD database, including 7,124 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.26 (4939 hom., cov: 22)
  • Exomes 𝑓: 0.24 (2185 hom.)
• Consequence: ASB10 NM_001142459.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.160

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 -16 ACMG points.

• BP6: Variant 7-151187179-C-CAG is Benign according to our data. Variant chr7-151187179-C-CAG is described in ClinVar as [Benign]. Clinvar id is 402398.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.-51_-50dupCT		5_prime_UTR_variant	1/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_001142460.1	c.-51_-50dupCT		5_prime_UTR_variant	1/5		NP_001135932.2
ASB10	NM_080871.4	c.271+271_271+272dupCT		intron_variant			NP_543147.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38552 AN: 150140 Hom.: 4933 Cov.: 22

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.238 AC: 317270 AN: 1333586 Hom.: 2185 Cov.: 0 AF XY: 0.236 AC XY: 155203 AN XY: 658378

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.192

Gnomad4 ASJ exome AF: 0.294

Gnomad4 EAS exome AF: 0.112

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.207

Gnomad4 NFE exome AF: 0.249

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.257 AC: 38583 AN: 150236 Hom.: 4939 Cov.: 22 AF XY: 0.251 AC XY: 18388 AN XY: 73366

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.0813

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.280

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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: Frequency -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

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;