rs1040399

Variant names:

• chrX-43766152-G-A
• rs1040399

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 0.028 in 111,335 control chromosomes in the GnomAD database, including 101 homozygotes. There are 1,005 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 0.028 (101 hom., 1005 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 0.0280 AC: 3113 AN: 111284 Hom.: 98 Cov.: 23 AF XY: 0.0300 AC XY: 1004 AN XY: 33492

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0212

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.00253

Gnomad MID AF: 0.00420

Gnomad NFE AF: 0.00339

Gnomad OTH AF: 0.0269

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

GnomAD4 genome AF: 0.0280 AC: 3120 AN: 111335 Hom.: 101 Cov.: 23 AF XY: 0.0300 AC XY: 1005 AN XY: 33553

Gnomad4 AFR AF: 0.0361

Gnomad4 AMR AF: 0.0669

Gnomad4 ASJ AF: 0.0212

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.00253

Gnomad4 NFE AF: 0.00339

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0267 Hom.: 120

Bravo AF: 0.0323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040399; hg19: chrX-43625399;