rs5984367

Variant names:

• chrX-89716138-C-A
• rs5984367

Your query was ambiguous. Multiple possible variants found:

• chrX-89716138-C-A
• chrX-89716138-C-T

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 0.092 in 110,542 control chromosomes in the GnomAD database, including 1,151 homozygotes. There are 2,732 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 0.092 (1151 hom., 2732 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.0919 AC: 10150 AN: 110504 Hom.: 1150 Cov.: 23

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0300

Gnomad NFE AF: 0.00102

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0920 AC: 10175 AN: 110542 Hom.: 1151 Cov.: 23 AF XY: 0.0830 AC XY: 2732 AN XY: 32902

African (AFR) AF: 0.319 AC: 9634 AN: 30197

American (AMR) AF: 0.0368 AC: 383 AN: 10419

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2639

East Asian (EAS) AF: 0.00 AC: 0 AN: 3531

South Asian (SAS) AF: 0.00113 AC: 3 AN: 2660

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5790

Middle Eastern (MID) AF: 0.0333 AC: 7 AN: 210

European-Non Finnish (NFE) AF: 0.00102 AC: 54 AN: 52901

Other (OTH) AF: 0.0623 AC: 94 AN: 1508

Alfa AF: 0.0504 Hom.: 1003

Bravo AF: 0.106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.8
DANN	Benign	0.87
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs5984367; hg19: chrX-88971137;