X-87008945-T-C

Variant names:

• chrX-87008945-T-C
• rs926686

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 0.533 in 110,769 control chromosomes in the GnomAD database, including 12,543 homozygotes. There are 17,236 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 0.53 (12543 hom., 17236 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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: 0.533 AC: 58987 AN: 110717 Hom.: 12537 Cov.: 23

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.533 AC: 59049 AN: 110769 Hom.: 12543 Cov.: 23 AF XY: 0.522 AC XY: 17236 AN XY: 33033

African (AFR) AF: 0.805 AC: 24479 AN: 30406

American (AMR) AF: 0.577 AC: 6013 AN: 10420

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1222 AN: 2633

East Asian (EAS) AF: 0.322 AC: 1121 AN: 3483

South Asian (SAS) AF: 0.568 AC: 1483 AN: 2611

European-Finnish (FIN) AF: 0.363 AC: 2150 AN: 5918

Middle Eastern (MID) AF: 0.452 AC: 95 AN: 210

European-Non Finnish (NFE) AF: 0.407 AC: 21538 AN: 52918

Other (OTH) AF: 0.524 AC: 783 AN: 1495

Alfa AF: 0.457 Hom.: 3528

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs926686; hg19: chrX-86263948;