rs7888189

chrX-140890995-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;