rs3813928

Variant names:

• chrX-114583809-G-A
• rs3813928

Variant summary

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

The variant allele was found at a frequency of 0.128 in 107,870 control chromosomes in the GnomAD database, including 756 homozygotes. There are 4,030 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.13 (756 hom., 4030 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant X-114583809-G-A is Benign according to our data. Variant chrX-114583809-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1318441.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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

Frequencies

GnomAD3 genomes AF: 0.128 AC: 13832 AN: 107817 Hom.: 757 Cov.: 21 AF XY: 0.132 AC XY: 4023 AN XY: 30475

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0311

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.128 AC: 13836 AN: 107870 Hom.: 756 Cov.: 21 AF XY: 0.132 AC XY: 4030 AN XY: 30538

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.129

Alfa AF: 0.162 Hom.: 3441

Bravo AF: 0.119

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 14, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 15741483, 16021472) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813928; hg19: chrX-113818282;