chr7-151187179-CAGAG-C

Position:

• chr7-151187179-CAGAG-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001142459.2(ASB10):​c.-53_-50delCTCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,488,790 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 0.000020 (0 hom., cov: 22)
  • Exomes 𝑓: 0.00017 (0 hom.)
• Consequence: ASB10 NM_001142459.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 223 AD gene.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0000200 AC: 3 AN: 150224 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000297

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000167 AC: 223 AN: 1338470 Hom.: 0 AF XY: 0.000210 AC XY: 139 AN XY: 660408

Gnomad4 AFR exome AF: 0.000231

Gnomad4 AMR exome AF: 0.000667

Gnomad4 ASJ exome AF: 0.000290

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000524

Gnomad4 FIN exome AF: 0.000255

Gnomad4 NFE exome AF: 0.000124

Gnomad4 OTH exome AF: 0.0000896

GnomAD4 genome AF: 0.0000200 AC: 3 AN: 150320 Hom.: 0 Cov.: 22 AF XY: 0.0000136 AC XY: 1 AN XY: 73394

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000297

Gnomad4 OTH AF: 0.00

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;