chrX-98410973-T-A

Position:

• chrX-98410973-T-A

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 0.31 in 110,889 control chromosomes in the GnomAD database, including 4,200 homozygotes. There are 10,340 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 0.31 (4200 hom., 10340 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 34325 AN: 110839 Hom.: 4210 Cov.: 23 AF XY: 0.311 AC XY: 10318 AN XY: 33139

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.310 AC: 34325 AN: 110889 Hom.: 4200 Cov.: 23 AF XY: 0.311 AC XY: 10340 AN XY: 33199

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.352

Alfa AF: 0.301 Hom.: 1902

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886827; hg19: chrX-97665971;