X-98369663-G-T

Variant names:

• chrX-98369663-G-T
• rs5920654

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 0.213 in 111,356 control chromosomes in the GnomAD database, including 1,920 homozygotes. There are 6,805 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 0.21 (1920 hom., 6805 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.213 AC: 23687 AN: 111303 Hom.: 1914 Cov.: 22 AF XY: 0.202 AC XY: 6786 AN XY: 33551

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.213 AC: 23710 AN: 111356 Hom.: 1920 Cov.: 22 AF XY: 0.202 AC XY: 6805 AN XY: 33614

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.215

Alfa AF: 0.176 Hom.: 1576

Bravo AF: 0.211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5920654; hg19: chrX-97624661;