rs2208906

Variant names:

• chrX-87773701-T-A
• rs2208906

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 0.136 in 111,555 control chromosomes in the GnomAD database, including 967 homozygotes. There are 4,318 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 0.14 (967 hom., 4318 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.136 AC: 15190 AN: 111499 Hom.: 966 Cov.: 23

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0612

Gnomad MID AF: 0.113

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.136 AC: 15200 AN: 111555 Hom.: 967 Cov.: 23 AF XY: 0.128 AC XY: 4318 AN XY: 33785

African (AFR) AF: 0.256 AC: 7868 AN: 30709

American (AMR) AF: 0.0561 AC: 589 AN: 10508

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 404 AN: 2642

East Asian (EAS) AF: 0.182 AC: 640 AN: 3514

South Asian (SAS) AF: 0.140 AC: 377 AN: 2699

European-Finnish (FIN) AF: 0.0612 AC: 370 AN: 6045

Middle Eastern (MID) AF: 0.119 AC: 25 AN: 210

European-Non Finnish (NFE) AF: 0.0871 AC: 4621 AN: 53031

Other (OTH) AF: 0.117 AC: 177 AN: 1519

Alfa AF: 0.118 Hom.: 648

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.47
DANN	Benign	0.54
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2208906; hg19: chrX-87028701;