chrX-15241993-C-A

Position:

• chrX-15241993-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000477346.6(ASB9):​c.506-5393G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 110,513 control chromosomes in the GnomAD database, including 7,393 homozygotes. There are 14,101 hemizygotes in GnomAD. 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 0.43 (7393 hom., 14101 hem., cov: 23)
• Consequence: ASB9 ENST00000477346.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15241993C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB9	ENST00000477346.6	c.506-5393G>T		intron_variant		2		ENSP00000473542.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 47378 AN: 110456 Hom.: 7386 Cov.: 23 AF XY: 0.430 AC XY: 14081 AN XY: 32722

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.429 AC: 47407 AN: 110513 Hom.: 7393 Cov.: 23 AF XY: 0.430 AC XY: 14101 AN XY: 32789

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.479

Alfa AF: 0.428 Hom.: 27029

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1383057; hg19: chrX-15260115;