rs1040398

Variant names:

• chrX-43766184-A-G
• rs1040398

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 0.0671 in 111,678 control chromosomes in the GnomAD database, including 460 homozygotes. There are 2,148 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 (460 hom., 2148 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 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: 0.0670 AC: 7474 AN: 111629 Hom.: 458 Cov.: 24 AF XY: 0.0631 AC XY: 2133 AN XY: 33791

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.00215

Gnomad MID AF: 0.00840

Gnomad NFE AF: 0.00370

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0671 AC: 7496 AN: 111678 Hom.: 460 Cov.: 24 AF XY: 0.0635 AC XY: 2148 AN XY: 33850

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.0211

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.00215

Gnomad4 NFE AF: 0.00370

Gnomad4 OTH AF: 0.0703

Alfa AF: 0.0169 Hom.: 918

Bravo AF: 0.0772

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040398; hg19: chrX-43625431;