rs1518519

Variant names:

• chrX-33627573-G-A
• rs1518519

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 0.375 in 110,832 control chromosomes in the GnomAD database, including 6,567 homozygotes. There are 12,418 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 0.38 (6567 hom., 12418 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 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: 0.375 AC: 41597 AN: 110780 Hom.: 6569 Cov.: 23

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.00678

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.375 AC: 41585 AN: 110832 Hom.: 6567 Cov.: 23 AF XY: 0.375 AC XY: 12418 AN XY: 33132

African (AFR) AF: 0.144 AC: 4421 AN: 30718

American (AMR) AF: 0.428 AC: 4453 AN: 10411

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1206 AN: 2625

East Asian (EAS) AF: 0.00708 AC: 25 AN: 3531

South Asian (SAS) AF: 0.320 AC: 859 AN: 2683

European-Finnish (FIN) AF: 0.589 AC: 3444 AN: 5848

Middle Eastern (MID) AF: 0.493 AC: 106 AN: 215

European-Non Finnish (NFE) AF: 0.497 AC: 26152 AN: 52616

Other (OTH) AF: 0.386 AC: 583 AN: 1511

Alfa AF: 0.456 Hom.: 37987

Bravo AF: 0.353

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.031
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1518519; hg19: chrX-33645690;