rs785787

Variant names:

• chrX-93072256-A-G
• rs785787

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 0.109 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.109 AC: 12140 AN: 111081 Hom.: 684 Cov.: 22

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

African (AFR) AF: 0.132 AC: 4041 AN: 30595

American (AMR) AF: 0.203 AC: 2116 AN: 10439

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 163 AN: 2643

East Asian (EAS) AF: 0.282 AC: 988 AN: 3504

South Asian (SAS) AF: 0.354 AC: 936 AN: 2646

European-Finnish (FIN) AF: 0.0350 AC: 208 AN: 5951

Middle Eastern (MID) AF: 0.0841 AC: 18 AN: 214

European-Non Finnish (NFE) AF: 0.0662 AC: 3505 AN: 52934

Other (OTH) AF: 0.114 AC: 173 AN: 1521

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs785787; hg19: chrX-92327255;