rs5969181

Variant names:

• chrX-87368646-G-A
• rs5969181

Your query was ambiguous. Multiple possible variants found:

• chrX-87368646-G-A
• chrX-87368646-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.363 in 109,889 control chromosomes in the GnomAD database, including 5,355 homozygotes. There are 11,403 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (5355 hom., 11403 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.363 AC: 39843 AN: 109842 Hom.: 5356 Cov.: 22

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.363 AC: 39849 AN: 109889 Hom.: 5355 Cov.: 22 AF XY: 0.354 AC XY: 11403 AN XY: 32221

African (AFR) AF: 0.339 AC: 10275 AN: 30266

American (AMR) AF: 0.248 AC: 2566 AN: 10350

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 817 AN: 2630

East Asian (EAS) AF: 0.592 AC: 2018 AN: 3409

South Asian (SAS) AF: 0.310 AC: 803 AN: 2593

European-Finnish (FIN) AF: 0.385 AC: 2173 AN: 5638

Middle Eastern (MID) AF: 0.305 AC: 64 AN: 210

European-Non Finnish (NFE) AF: 0.385 AC: 20265 AN: 52625

Other (OTH) AF: 0.344 AC: 518 AN: 1507

Alfa AF: 0.357 Hom.: 29479

Bravo AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs5969181; hg19: chrX-86623649;