rs5909876

Variant names:

• chrX-122088395-G-A
• rs5909876

Your query was ambiguous. Multiple possible variants found:

• chrX-122088395-G-A
• chrX-122088395-G-C

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 0.25 in 110,783 control chromosomes in the GnomAD database, including 3,039 homozygotes. There are 8,433 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 0.25 (3039 hom., 8433 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.250 AC: 27662 AN: 110730 Hom.: 3040 Cov.: 23

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.250 AC: 27659 AN: 110783 Hom.: 3039 Cov.: 23 AF XY: 0.255 AC XY: 8433 AN XY: 33067

African (AFR) AF: 0.0632 AC: 1937 AN: 30650

American (AMR) AF: 0.266 AC: 2758 AN: 10357

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 605 AN: 2645

East Asian (EAS) AF: 0.562 AC: 1951 AN: 3473

South Asian (SAS) AF: 0.480 AC: 1274 AN: 2655

European-Finnish (FIN) AF: 0.355 AC: 2066 AN: 5820

Middle Eastern (MID) AF: 0.255 AC: 54 AN: 212

European-Non Finnish (NFE) AF: 0.313 AC: 16519 AN: 52780

Other (OTH) AF: 0.243 AC: 368 AN: 1515

Alfa AF: 0.257 Hom.: 2547

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.81
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs5909876; hg19: chrX-121222248;