rs3092952

Variant names:

• chrX-136644791-A-G
• rs3092952

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.283 AC: 31526 AN: 111462 Hom.: 3975 Cov.: 23

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

African (AFR) AF: 0.467 AC: 14250 AN: 30521

American (AMR) AF: 0.416 AC: 4394 AN: 10571

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 438 AN: 2649

East Asian (EAS) AF: 0.0830 AC: 296 AN: 3567

South Asian (SAS) AF: 0.336 AC: 905 AN: 2690

European-Finnish (FIN) AF: 0.184 AC: 1106 AN: 5995

Middle Eastern (MID) AF: 0.274 AC: 59 AN: 215

European-Non Finnish (NFE) AF: 0.182 AC: 9652 AN: 53097

Other (OTH) AF: 0.286 AC: 435 AN: 1523

Alfa AF: 0.246 Hom.: 7500

Bravo AF: 0.313

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 13, 2022

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs3092952; hg19: chrX-135726950;