rs2781516

Variant names:

• chrX-67882189-G-A
• rs2781516

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 0.312 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.312 AC: 34526 AN: 110644 Hom.: 6014 Cov.: 22

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

African (AFR) AF: 0.679 AC: 20596 AN: 30340

American (AMR) AF: 0.177 AC: 1836 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 457 AN: 2641

East Asian (EAS) AF: 0.00170 AC: 6 AN: 3527

South Asian (SAS) AF: 0.0876 AC: 233 AN: 2661

European-Finnish (FIN) AF: 0.157 AC: 929 AN: 5901

Middle Eastern (MID) AF: 0.319 AC: 69 AN: 216

European-Non Finnish (NFE) AF: 0.188 AC: 9944 AN: 52868

Other (OTH) AF: 0.280 AC: 419 AN: 1494

Alfa AF: 0.240 Hom.: 6900

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2781516; hg19: chrX-67102031;