rs1040398

Variant names:

• chrX-43766184-A-G
• rs1040398

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 0.0671 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.172 AC: 5277 AN: 30620

American (AMR) AF: 0.0808 AC: 851 AN: 10529

Ashkenazi Jewish (ASJ) AF: 0.0211 AC: 56 AN: 2651

East Asian (EAS) AF: 0.148 AC: 522 AN: 3538

South Asian (SAS) AF: 0.179 AC: 472 AN: 2644

European-Finnish (FIN) AF: 0.00215 AC: 13 AN: 6047

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.00370 AC: 197 AN: 53227

Other (OTH) AF: 0.0703 AC: 107 AN: 1522

Alfa AF: 0.0306 Hom.: 2239

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1040398; hg19: chrX-43625431;