rs785787

Positions:

• chrX-93072256-A-G

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 0.109 in 111,132 control chromosomes in the GnomAD database, including 685 homozygotes. There are 3,683 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 0.11 (685 hom., 3683 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.109 AC: 12140 AN: 111081 Hom.: 684 Cov.: 22 AF XY: 0.110 AC XY: 3662 AN XY: 33367

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0851

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 12163 AN: 111132 Hom.: 685 Cov.: 22 AF XY: 0.110 AC XY: 3683 AN XY: 33428

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.0350

Gnomad4 NFE AF: 0.0662

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0130 Hom.: 50

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs785787; hg19: chrX-92327255;