rs2207081

Variant names:

• chrX-67353856-T-C
• rs2207081

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.360 AC: 40148 AN: 111369 Hom.: 9224 Cov.: 23 AF XY: 0.337 AC XY: 11300 AN XY: 33581

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

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.00169

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.312

Alfa AF: 0.235 Hom.: 2320

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207081; hg19: chrX-66573698;