rs7882595

Positions:

• chrX-140531481-G-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 0.219 in 110,457 control chromosomes in the GnomAD database, including 3,287 homozygotes. There are 6,472 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 0.22 (3287 hom., 6472 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 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: 0.218 AC: 24098 AN: 110405 Hom.: 3284 Cov.: 22 AF XY: 0.197 AC XY: 6435 AN XY: 32679

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.219 AC: 24146 AN: 110457 Hom.: 3287 Cov.: 22 AF XY: 0.198 AC XY: 6472 AN XY: 32741

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.0283

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.207

Alfa AF: 0.185 Hom.: 1114

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7882595; hg19: chrX-139613646;