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. The variant received -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
• Publications: 1 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000477346.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB9	ENST00000477346.6	TSL:2	c.506-5393G>T		intron	N/A	ENSP00000473542.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 47378 AN: 110456 Hom.: 7386 Cov.: 23

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

African (AFR) AF: 0.395 AC: 11991 AN: 30324

American (AMR) AF: 0.510 AC: 5262 AN: 10308

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1122 AN: 2625

East Asian (EAS) AF: 0.776 AC: 2735 AN: 3526

South Asian (SAS) AF: 0.524 AC: 1368 AN: 2610

European-Finnish (FIN) AF: 0.381 AC: 2239 AN: 5880

Middle Eastern (MID) AF: 0.442 AC: 95 AN: 215

European-Non Finnish (NFE) AF: 0.411 AC: 21742 AN: 52843

Other (OTH) AF: 0.479 AC: 719 AN: 1502

Alfa AF: 0.428 Hom.: 40031

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.77
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs1383057; hg19: chrX-15260115;