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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.552 AC: 60132 AN: 108947 Hom.: 13468 Cov.: 21 AF XY: 0.532 AC XY: 16647 AN XY: 31299

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

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.526

Alfa AF: 0.496 Hom.: 11841

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7882767; hg19: chrX-84889054;