rs7888189

Variant names:

• chrX-140890995-T-C
• rs7888189

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 0.0871 in 111,869 control chromosomes in the GnomAD database, including 452 homozygotes. There are 2,776 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 0.087 (452 hom., 2776 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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: 0.0870 AC: 9733 AN: 111814 Hom.: 452 Cov.: 23

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0160

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0553

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0871 AC: 9740 AN: 111869 Hom.: 452 Cov.: 23 AF XY: 0.0815 AC XY: 2776 AN XY: 34081

African (AFR) AF: 0.184 AC: 5655 AN: 30748

American (AMR) AF: 0.0553 AC: 583 AN: 10548

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 156 AN: 2650

East Asian (EAS) AF: 0.00 AC: 0 AN: 3570

South Asian (SAS) AF: 0.0209 AC: 56 AN: 2678

European-Finnish (FIN) AF: 0.0579 AC: 353 AN: 6093

Middle Eastern (MID) AF: 0.0469 AC: 10 AN: 213

European-Non Finnish (NFE) AF: 0.0524 AC: 2786 AN: 53162

Other (OTH) AF: 0.0855 AC: 130 AN: 1521

Alfa AF: 0.0671 Hom.: 4529

Bravo AF: 0.0937

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.65
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7888189; hg19: chrX-139973160;