rs3092952

Positions:

• chrX-136644791-A-G

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 0.283 in 111,513 control chromosomes in the GnomAD database, including 3,978 homozygotes. There are 9,363 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (3978 hom., 9363 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.150

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant X-136644791-A-G is Benign according to our data. Variant chrX-136644791-A-G is described in ClinVar as [Benign]. Clinvar id is 810925.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.283 AC: 31526 AN: 111462 Hom.: 3975 Cov.: 23 AF XY: 0.277 AC XY: 9326 AN XY: 33666

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.0540

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.283 AC: 31572 AN: 111513 Hom.: 3978 Cov.: 23 AF XY: 0.278 AC XY: 9363 AN XY: 33727

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0830

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.286

Alfa AF: 0.228 Hom.: 4435

Bravo AF: 0.313

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

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Sep 13, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3092952; hg19: chrX-135726950;