rs1040399

Variant names:

• chrX-43766152-G-A
• rs1040399

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 0.028 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0361 AC: 1108 AN: 30661

American (AMR) AF: 0.0669 AC: 701 AN: 10472

Ashkenazi Jewish (ASJ) AF: 0.0212 AC: 56 AN: 2643

East Asian (EAS) AF: 0.150 AC: 526 AN: 3510

South Asian (SAS) AF: 0.184 AC: 479 AN: 2607

European-Finnish (FIN) AF: 0.00253 AC: 15 AN: 5921

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 216

European-Non Finnish (NFE) AF: 0.00339 AC: 180 AN: 53113

Other (OTH) AF: 0.0365 AC: 55 AN: 1508

Alfa AF: 0.0261 Hom.: 137

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1040399; hg19: chrX-43625399;