7-151187179-CAGAGAG-CAGAGAGAGAG

Position:

• chr7-151187179-CAGAGAG-CAGAGAGAGAG

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting

The NM_001142459.2(ASB10):​c.-53_-50dupCTCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,495,042 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000067 (0 hom., cov: 22)
  • Exomes 𝑓: 0.00019 (0 hom.)
• Consequence: ASB10 NM_001142459.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -1 ACMG points.

• BS2: High AC in GnomAd4 at 10 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.-53_-50dupCTCT		5_prime_UTR_variant	1/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_001142460.1	c.-53_-50dupCTCT		5_prime_UTR_variant	1/5		NP_001135932.2
ASB10	NM_080871.4	c.271+269_271+272dupCTCT		intron_variant			NP_543147.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175.3	c.-53_-50dupCTCT		5_prime_UTR_variant	1/6	1	NM_001142459.2	ENSP00000391137.2
ASB10	ENST00000275838.5	c.-53_-50dupCTCT		5_prime_UTR_variant	1/5	1		ENSP00000275838.1
ASB10	ENST00000377867.7	c.271+269_271+272dupCTCT		intron_variant		2		ENSP00000367098.3
ASB10	ENST00000415615.1	n.*121+71_*121+74dupCTCT		intron_variant		4		ENSP00000410871.1

Frequencies

GnomAD3 genomes AF: 0.0000666 AC: 10 AN: 150242 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.0000976

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000741

Gnomad OTH AF: 0.000484

GnomAD4 exome AF: 0.000190 AC: 255 AN: 1344800 Hom.: 0 Cov.: 0 AF XY: 0.000209 AC XY: 139 AN XY: 663796

Gnomad4 AFR exome AF: 0.000262

Gnomad4 AMR exome AF: 0.0000574

Gnomad4 ASJ exome AF: 0.000165

Gnomad4 EAS exome AF: 0.0000576

Gnomad4 SAS exome AF: 0.000143

Gnomad4 FIN exome AF: 0.000126

Gnomad4 NFE exome AF: 0.000210

Gnomad4 OTH exome AF: 0.0000892

GnomAD4 genome AF: 0.0000666 AC: 10 AN: 150242 Hom.: 0 Cov.: 22 AF XY: 0.0000546 AC XY: 4 AN XY: 73300

Gnomad4 AFR AF: 0.0000976

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000741

Gnomad4 OTH AF: 0.000484

ClinVar

Not reported in ClinVar

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;