rs1040400

Positions:

• chrX-43766089-A-G

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 0.0675 in 111,753 control chromosomes in the GnomAD database, including 456 homozygotes. There are 2,196 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 0.067 (456 hom., 2196 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 7519 AN: 111698 Hom.: 454 Cov.: 23 AF XY: 0.0644 AC XY: 2183 AN XY: 33898

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0212

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.00248

Gnomad MID AF: 0.00840

Gnomad NFE AF: 0.00367

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0675 AC: 7539 AN: 111753 Hom.: 456 Cov.: 23 AF XY: 0.0647 AC XY: 2196 AN XY: 33963

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.0212

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.00248

Gnomad4 NFE AF: 0.00367

Gnomad4 OTH AF: 0.0675

Alfa AF: 0.0388 Hom.: 182

Bravo AF: 0.0772

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.90
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040400; hg19: chrX-43625336;