rs6527396

Positions:

• chrX-15253849-C-A

Variant summary

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

The NM_001031739.3(ASB9):​c.282+888G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 110,795 control chromosomes in the GnomAD database, including 2,346 homozygotes. There are 5,980 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 0.19 (2346 hom., 5980 hem., cov: 22)
• Consequence: ASB9 NM_001031739.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASB9	NM_001031739.3	c.282+888G>T		intron_variant		ENST00000380488.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASB9	ENST00000380488.9	c.282+888G>T		intron_variant		1	NM_001031739.3	P1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 21302 AN: 110740 Hom.: 2349 Cov.: 22 AF XY: 0.181 AC XY: 5958 AN XY: 32986

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0146

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.192 AC: 21311 AN: 110795 Hom.: 2346 Cov.: 22 AF XY: 0.181 AC XY: 5980 AN XY: 33051

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.176

Alfa AF: 0.113 Hom.: 8321

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.66

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: rs6527396; hg19: chrX-15271971;