rs2207081

Variant names:

• chrX-67353856-T-C
• rs2207081

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 0.361 in 111,421 control chromosomes in the GnomAD database, including 9,234 homozygotes. There are 11,350 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 0.36 (9234 hom., 11350 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.360 AC: 40148 AN: 111369 Hom.: 9224 Cov.: 23

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00168

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.361 AC: 40212 AN: 111421 Hom.: 9234 Cov.: 23 AF XY: 0.337 AC XY: 11350 AN XY: 33643

African (AFR) AF: 0.865 AC: 26390 AN: 30524

American (AMR) AF: 0.176 AC: 1855 AN: 10515

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 274 AN: 2646

East Asian (EAS) AF: 0.00169 AC: 6 AN: 3557

South Asian (SAS) AF: 0.0818 AC: 223 AN: 2727

European-Finnish (FIN) AF: 0.176 AC: 1058 AN: 5995

Middle Eastern (MID) AF: 0.253 AC: 55 AN: 217

European-Non Finnish (NFE) AF: 0.185 AC: 9796 AN: 53040

Other (OTH) AF: 0.312 AC: 475 AN: 1522

Alfa AF: 0.255 Hom.: 7395

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.54
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2207081; hg19: chrX-66573698;