rs1383057

Variant names:

• chrX-15241993-C-A
• rs1383057
• ENST00000477346.6:c.506-5393G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-15241993-C-A
• chrX-15241993-C-G
• chrX-15241993-C-T

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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB9	ENST00000477346.6	c.506-5393G>T		intron_variant	Intron 4 of 5	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;