rs1479927

chrX-15264700-G-AchrX-15264700-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001031739.3(ASB9):c.94+5081C>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 0.58 (13173 hom., 18924 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ASB9 NM_001031739.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS2: High Homozygotes in GnomAd at 13181 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB9	NM_001031739.3	c.94+5081C>T		intron_variant		ENST00000380488.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB9	ENST00000380488.9	c.94+5081C>T		intron_variant		1	NM_001031739.3	P1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 63963 AN: 110132 Hom.: 13181 Cov.: 22 AF XY: 0.583 AC XY: 18885 AN XY: 32404

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.603

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: 0.581 AC: 63984 AN: 110187 Hom.: 13173 Cov.: 22 AF XY: 0.583 AC XY: 18924 AN XY: 32469

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.598

Alfa AF: 0.595 Hom.: 39053

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.61

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: rs1479927; hg19: chrX-15282822;