rs760867

chrX-66160441-T-C

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 0.326 in 111,123 control chromosomes in the GnomAD database, including 8,092 homozygotes. There are 10,212 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 0.33 (8092 hom., 10212 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.326 AC: 36155 AN: 111071 Hom.: 8085 Cov.: 23 AF XY: 0.305 AC XY: 10158 AN XY: 33331

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000851

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.326 AC: 36221 AN: 111123 Hom.: 8092 Cov.: 23 AF XY: 0.306 AC XY: 10212 AN XY: 33393

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.000853

Gnomad4 SAS AF: 0.0908

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.266

Alfa AF: 0.188 Hom.: 3869

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
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: rs760867; hg19: chrX-65380283;