rs2781516

Positions:

• chrX-67882189-G-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 0.312 in 110,699 control chromosomes in the GnomAD database, including 6,021 homozygotes. There are 9,651 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 (6021 hom., 9651 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.312 AC: 34526 AN: 110644 Hom.: 6014 Cov.: 22 AF XY: 0.292 AC XY: 9615 AN XY: 32942

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00170

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.312 AC: 34575 AN: 110699 Hom.: 6021 Cov.: 22 AF XY: 0.292 AC XY: 9651 AN XY: 33007

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00170

Gnomad4 SAS AF: 0.0876

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.280

Alfa AF: 0.230 Hom.: 2616

Bravo AF: 0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2781516; hg19: chrX-67102031;