X-15247335-G-A

Variant names:

• chrX-15247335-G-A
• rs2291122
• NM_001031739.3:c.760+1409C>T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031739.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB9	NM_001031739.3	MANE Select	c.760+1409C>T		intron	N/A	NP_001026909.1	Q96DX5-1
	ASB9	NM_001168531.2		c.*32+1348C>T		intron	N/A	NP_001162003.1	Q96DX5-2
	ASB9	NM_024087.3		c.*32+1348C>T		intron	N/A	NP_076992.1	Q96DX5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB9	ENST00000380488.9	TSL:1 MANE Select	c.760+1409C>T		intron	N/A	ENSP00000369855.4	Q96DX5-1
	ASB9	ENST00000380485.7	TSL:1	c.*32+1348C>T		intron	N/A	ENSP00000369852.3	Q96DX5-2
	ASB9	ENST00000380483.7	TSL:1	c.*32+1348C>T		intron	N/A	ENSP00000369850.3	Q96DX5-3

Frequencies

GnomAD3 genomes AF: 0.521 AC: 57510 AN: 110441 Hom.: 11245 Cov.: 23

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

African (AFR) AF: 0.675 AC: 20437 AN: 30292

American (AMR) AF: 0.440 AC: 4602 AN: 10453

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1058 AN: 2629

East Asian (EAS) AF: 0.309 AC: 1071 AN: 3467

South Asian (SAS) AF: 0.462 AC: 1184 AN: 2565

European-Finnish (FIN) AF: 0.481 AC: 2821 AN: 5864

Middle Eastern (MID) AF: 0.491 AC: 106 AN: 216

European-Non Finnish (NFE) AF: 0.473 AC: 25002 AN: 52835

Other (OTH) AF: 0.495 AC: 742 AN: 1500

Alfa AF: 0.484 Hom.: 60212

Bravo AF: 0.525

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2291122; hg19: chrX-15265457;