rs2168035

Variant names:

• chrX-28562233-G-A
• rs2168035

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 0.0809 in 111,385 control chromosomes in the GnomAD database, including 366 homozygotes. There are 2,665 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 0.081 (366 hom., 2665 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 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: 0.0808 AC: 9001 AN: 111332 Hom.: 366 Cov.: 23

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0809 AC: 9006 AN: 111385 Hom.: 366 Cov.: 23 AF XY: 0.0793 AC XY: 2665 AN XY: 33611

African (AFR) AF: 0.0161 AC: 494 AN: 30724

American (AMR) AF: 0.0569 AC: 596 AN: 10477

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 385 AN: 2640

East Asian (EAS) AF: 0.00 AC: 0 AN: 3529

South Asian (SAS) AF: 0.0309 AC: 82 AN: 2653

European-Finnish (FIN) AF: 0.155 AC: 920 AN: 5933

Middle Eastern (MID) AF: 0.157 AC: 34 AN: 216

European-Non Finnish (NFE) AF: 0.118 AC: 6271 AN: 53010

Other (OTH) AF: 0.0829 AC: 126 AN: 1520

Alfa AF: 0.0872 Hom.: 2659

Bravo AF: 0.0736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.68
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2168035; hg19: chrX-28580350;