rs7879492

Variant names:

• chrX-85763620-G-A
• rs7879492

Your query was ambiguous. Multiple possible variants found:

• chrX-85763620-G-A
• chrX-85763620-G-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 0.451 in 110,211 control chromosomes in the GnomAD database, including 8,573 homozygotes. There are 14,719 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 0.45 (8573 hom., 14719 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 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: 0.451 AC: 49706 AN: 110159 Hom.: 8572 Cov.: 23

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.451 AC: 49709 AN: 110211 Hom.: 8573 Cov.: 23 AF XY: 0.453 AC XY: 14719 AN XY: 32503

African (AFR) AF: 0.275 AC: 8372 AN: 30458

American (AMR) AF: 0.629 AC: 6473 AN: 10288

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 923 AN: 2623

East Asian (EAS) AF: 0.498 AC: 1719 AN: 3453

South Asian (SAS) AF: 0.394 AC: 1019 AN: 2589

European-Finnish (FIN) AF: 0.642 AC: 3704 AN: 5772

Middle Eastern (MID) AF: 0.406 AC: 86 AN: 212

European-Non Finnish (NFE) AF: 0.503 AC: 26466 AN: 52648

Other (OTH) AF: 0.464 AC: 695 AN: 1497

Alfa AF: 0.481 Hom.: 17612

Bravo AF: 0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7879492; hg19: chrX-85018625;