chrX-43766089-A-G

Variant names:

• chrX-43766089-A-G
• rs1040400

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 0.0675 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 7519 AN: 111698 Hom.: 454 Cov.: 23

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

African (AFR) AF: 0.173 AC: 5310 AN: 30671

American (AMR) AF: 0.0798 AC: 843 AN: 10561

Ashkenazi Jewish (ASJ) AF: 0.0212 AC: 56 AN: 2646

East Asian (EAS) AF: 0.149 AC: 529 AN: 3544

South Asian (SAS) AF: 0.183 AC: 487 AN: 2654

European-Finnish (FIN) AF: 0.00248 AC: 15 AN: 6058

Middle Eastern (MID) AF: 0.00461 AC: 1 AN: 217

European-Non Finnish (NFE) AF: 0.00367 AC: 195 AN: 53189

Other (OTH) AF: 0.0675 AC: 103 AN: 1525

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1040400; hg19: chrX-43625336;