chrX-67018503-C-T

Variant names:

• chrX-67018503-C-T
• rs521362

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 0.337 in 110,313 control chromosomes in the GnomAD database, including 8,588 homozygotes. There are 10,248 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 0.34 (8588 hom., 10248 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.337 AC: 37149 AN: 110264 Hom.: 8577 Cov.: 22

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0797

Gnomad EAS AF: 0.00142

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.337 AC: 37210 AN: 110313 Hom.: 8588 Cov.: 22 AF XY: 0.314 AC XY: 10248 AN XY: 32631

African (AFR) AF: 0.843 AC: 25389 AN: 30129

American (AMR) AF: 0.162 AC: 1687 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.0797 AC: 210 AN: 2634

East Asian (EAS) AF: 0.00143 AC: 5 AN: 3502

South Asian (SAS) AF: 0.0767 AC: 200 AN: 2609

European-Finnish (FIN) AF: 0.162 AC: 951 AN: 5868

Middle Eastern (MID) AF: 0.233 AC: 50 AN: 215

European-Non Finnish (NFE) AF: 0.155 AC: 8208 AN: 52787

Other (OTH) AF: 0.289 AC: 432 AN: 1495

Alfa AF: 0.190 Hom.: 3576

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.41
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs521362; hg19: chrX-66238345;