chrX-120469590-A-C

Position:

• chrX-120469590-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1636 hom., 2808 hem., cov: 19)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP6: Variant X-120469590-A-C is Benign according to our data. Variant chrX-120469590-A-C is described in ClinVar as [Benign]. Clinvar id is 683597.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 12852 AN: 102712 Hom.: 1631 Cov.: 19 AF XY: 0.105 AC XY: 2794 AN XY: 26566

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.0175

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.0447

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0913

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.125 AC: 12879 AN: 102735 Hom.: 1636 Cov.: 19 AF XY: 0.106 AC XY: 2808 AN XY: 26595

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.0687

Gnomad4 ASJ AF: 0.0175

Gnomad4 EAS AF: 0.0572

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0253

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0807 Hom.: 453

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	9.3
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28603270; hg19: chrX-119603445;