rs693642

Variant names:

• chrX-74365922-G-A
• rs693642

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 0.519 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.519 AC: 56935 AN: 109726 Hom.: 11382 Cov.: 22 AF XY: 0.500 AC XY: 16008 AN XY: 32040

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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.0488

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.573

Alfa AF: 0.555 Hom.: 4115

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs693642; hg19: chrX-73585757;