X-74365922-G-A

Variant names:

• chrX-74365922-G-A
• rs693642

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 0.519 in 109,783 control chromosomes in the GnomAD database, including 11,375 homozygotes. There are 16,025 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 0.52 (11375 hom., 16025 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 56935 AN: 109726 Hom.: 11382 Cov.: 22

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.519 AC: 56926 AN: 109783 Hom.: 11375 Cov.: 22 AF XY: 0.499 AC XY: 16025 AN XY: 32107

African (AFR) AF: 0.439 AC: 13214 AN: 30132

American (AMR) AF: 0.593 AC: 6058 AN: 10215

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 1692 AN: 2616

East Asian (EAS) AF: 0.0488 AC: 172 AN: 3527

South Asian (SAS) AF: 0.362 AC: 915 AN: 2531

European-Finnish (FIN) AF: 0.446 AC: 2550 AN: 5721

Middle Eastern (MID) AF: 0.676 AC: 146 AN: 216

European-Non Finnish (NFE) AF: 0.586 AC: 30863 AN: 52670

Other (OTH) AF: 0.573 AC: 852 AN: 1486

Alfa AF: 0.555 Hom.: 4115

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs693642; hg19: chrX-73585757;