rs1040398

chrX-43766184-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 0.0671 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;