rs2291122

Positions:

• chrX-15247335-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001031739.3(ASB9):​c.760+1409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (11237 hom., 16730 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ASB9 NM_001031739.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

Genes affected

ASB9 (HGNC:17184): (ankyrin repeat and SOCS box containing 9) This gene encodes a member of the ankyrin repeat and suppressor of cytokine signaling (SOCS) box protein family. Members of this family can interact with the elongin B-C adapter complex via their SOCS box domain and further complex with the cullin and ring box proteins to form E3 ubiquitin ligase complexes. They may function to mediate the substrate-recognition of the E3 ubiquitin ligases. A transcribed pseudogene of this gene has been identified on chromosome 15. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

ASB9 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB9	NM_001031739.3	c.760+1409C>T		intron_variant		ENST00000380488.9	NP_001026909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB9	ENST00000380488.9	c.760+1409C>T		intron_variant		1	NM_001031739.3	ENSP00000369855.4

Frequencies

GnomAD3 genomes AF: 0.521 AC: 57510 AN: 110441 Hom.: 11245 Cov.: 23 AF XY: 0.510 AC XY: 16687 AN XY: 32707

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.504

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.500

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.521 AC: 57535 AN: 110495 Hom.: 11237 Cov.: 23 AF XY: 0.511 AC XY: 16730 AN XY: 32771

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.495

Alfa AF: 0.472 Hom.: 48906

Bravo AF: 0.525

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2291122; hg19: chrX-15265457;