rs184407021

Positions:

• chrX-18425432-C-G
• chrX-18425432-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS2

The variant allele was found at a frequency of 0.00326 in 113,139 control chromosomes in the GnomAD database, including 1 homozygotes. There are 102 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.0033 (1 hom., 102 hem., cov: 25)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant X-18425432-C-G is Benign according to our data. Variant chrX-18425432-C-G is described in ClinVar as [Benign]. Clinvar id is 189539.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High Hemizygotes in GnomAd4 at 102 gene

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: 0.00327 AC: 370 AN: 113089 Hom.: 1 Cov.: 25 AF XY: 0.00289 AC XY: 102 AN XY: 35239

Gnomad AFR AF: 0.000674

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00343

Gnomad ASJ AF: 0.0165

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000717

Gnomad FIN AF: 0.00238

Gnomad MID AF: 0.0167

Gnomad NFE AF: 0.00429

Gnomad OTH AF: 0.0117

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

GnomAD4 genome AF: 0.00326 AC: 369 AN: 113139 Hom.: 1 Cov.: 25 AF XY: 0.00289 AC XY: 102 AN XY: 35299

Gnomad4 AFR AF: 0.000672

Gnomad4 AMR AF: 0.00342

Gnomad4 ASJ AF: 0.0165

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000719

Gnomad4 FIN AF: 0.00238

Gnomad4 NFE AF: 0.00429

Gnomad4 OTH AF: 0.0116

Alfa AF: 0.00114 Hom.: 7

Bravo AF: 0.00339

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

not specified Benign:1

Benign, no assertion criteria provided

curation

RettBASE

May 09, 2014

Found in normal population -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs184407021; hg19: chrX-18443552;