X-85763620-G-A

Variant names:

• chrX-85763620-G-A
• rs7879492

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 0.451 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.451 AC: 49706 AN: 110159 Hom.: 8572 Cov.: 23 AF XY: 0.454 AC XY: 14720 AN XY: 32441

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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.464

Alfa AF: 0.484 Hom.: 11904

Bravo AF: 0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7879492; hg19: chrX-85018625;