rs7888189

Variant names:

• chrX-140890995-T-C
• rs7888189

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0870 AC: 9733 AN: 111814 Hom.: 452 Cov.: 23 AF XY: 0.0813 AC XY: 2767 AN XY: 34016

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

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.0553

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0579

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0607 Hom.: 2875

Bravo AF: 0.0937

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7888189; hg19: chrX-139973160;