X-122339022-T-C

Variant names:

• chrX-122339022-T-C
• rs2495699

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 0.41 in 111,288 control chromosomes in the GnomAD database, including 9,271 homozygotes. There are 13,122 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 0.41 (9271 hom., 13122 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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: 0.410 AC: 45603 AN: 111232 Hom.: 9269 Cov.: 23

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.410 AC: 45658 AN: 111288 Hom.: 9271 Cov.: 23 AF XY: 0.391 AC XY: 13122 AN XY: 33534

African (AFR) AF: 0.808 AC: 24658 AN: 30532

American (AMR) AF: 0.307 AC: 3217 AN: 10465

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 731 AN: 2643

East Asian (EAS) AF: 0.177 AC: 623 AN: 3521

South Asian (SAS) AF: 0.195 AC: 531 AN: 2721

European-Finnish (FIN) AF: 0.240 AC: 1431 AN: 5961

Middle Eastern (MID) AF: 0.327 AC: 70 AN: 214

European-Non Finnish (NFE) AF: 0.260 AC: 13763 AN: 53020

Other (OTH) AF: 0.378 AC: 577 AN: 1527

Alfa AF: 0.308 Hom.: 34731

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.55
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs2495699; hg19: chrX-121472875;