rs34383739

chr7-151187179-CAGAGAG-Cchr7-151187179-CAGAGAG-CAGchr7-151187179-CAGAGAG-CAGAGchr7-151187179-CAGAGAG-CAGAGAGAGchr7-151187179-CAGAGAG-CAGAGAGAGAGchr7-151187179-CAGAGAG-CAGAGAGAGAGAG

Variant summary

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

The NM_001142459.2(ASB10):c.-55_-50del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000808 in 1,497,150 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 0.00045 (0 hom., cov: 22)
  • Exomes 𝑓: 0.000040 (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 GnomAd at 67 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB10	NM_001142459.2	c.-55_-50del		5_prime_UTR_variant	1/6	ENST00000420175.3
ASB10	NM_001142460.1	c.-55_-50del		5_prime_UTR_variant	1/5
ASB10	NM_080871.4	c.271+267_271+272del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB10	ENST00000420175.3	c.-55_-50del		5_prime_UTR_variant	1/6	1	NM_001142459.2	P4
ASB10	ENST00000275838.5	c.-55_-50del		5_prime_UTR_variant	1/5	1
ASB10	ENST00000377867.7	c.271+267_271+272del		intron_variant		2		A1
ASB10	ENST00000415615.1	c.*121+69_*121+74del		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.000446 AC: 67 AN: 150248 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000397

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: 0.0000148

Gnomad OTH AF: 0.00145

GnomAD4 exome AF: 0.0000401 AC: 54 AN: 1346804 Hom.: 0 AF XY: 0.0000271 AC XY: 18 AN XY: 664724

Gnomad4 AFR exome AF: 0.00111

Gnomad4 AMR exome AF: 0.0000861

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000135

Gnomad4 OTH exome AF: 0.0000535

GnomAD4 genome AF: 0.000446 AC: 67 AN: 150346 Hom.: 0 Cov.: 22 AF XY: 0.000463 AC XY: 34 AN XY: 73416

Gnomad4 AFR AF: 0.00139

Gnomad4 AMR AF: 0.000397

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000148

Gnomad4 OTH AF: 0.00144

Bravo AF: 0.000400

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;