rs7882767

Variant names:

• chrX-85634049-C-A
• rs7882767

Your query was ambiguous. Multiple possible variants found:

• chrX-85634049-C-A
• chrX-85634049-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 0.552 in 108,977 control chromosomes in the GnomAD database, including 13,463 homozygotes. There are 16,685 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 0.55 (13463 hom., 16685 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.552 AC: 60132 AN: 108947 Hom.: 13468 Cov.: 21

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.565

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.552 AC: 60157 AN: 108977 Hom.: 13463 Cov.: 21 AF XY: 0.532 AC XY: 16685 AN XY: 31339

African (AFR) AF: 0.821 AC: 24564 AN: 29919

American (AMR) AF: 0.350 AC: 3570 AN: 10204

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 1638 AN: 2626

East Asian (EAS) AF: 0.427 AC: 1459 AN: 3417

South Asian (SAS) AF: 0.518 AC: 1325 AN: 2558

European-Finnish (FIN) AF: 0.330 AC: 1804 AN: 5461

Middle Eastern (MID) AF: 0.563 AC: 117 AN: 208

European-Non Finnish (NFE) AF: 0.469 AC: 24576 AN: 52419

Other (OTH) AF: 0.526 AC: 782 AN: 1488

Alfa AF: 0.508 Hom.: 18541

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7882767; hg19: chrX-84889054;