rs1905182

Variant names:

• chrX-83340910-A-C
• rs1905182

Your query was ambiguous. Multiple possible variants found:

• chrX-83340910-A-C
• chrX-83340910-A-G

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 0.209 in 111,170 control chromosomes in the GnomAD database, including 2,024 homozygotes. There are 7,103 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 0.21 (2024 hom., 7103 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.210 AC: 23286 AN: 111122 Hom.: 2025 Cov.: 23

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.209 AC: 23263 AN: 111170 Hom.: 2024 Cov.: 23 AF XY: 0.213 AC XY: 7103 AN XY: 33378

African (AFR) AF: 0.0732 AC: 2251 AN: 30757

American (AMR) AF: 0.168 AC: 1756 AN: 10459

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 788 AN: 2631

East Asian (EAS) AF: 0.273 AC: 952 AN: 3488

South Asian (SAS) AF: 0.200 AC: 532 AN: 2658

European-Finnish (FIN) AF: 0.406 AC: 2365 AN: 5819

Middle Eastern (MID) AF: 0.221 AC: 47 AN: 213

European-Non Finnish (NFE) AF: 0.267 AC: 14110 AN: 52935

Other (OTH) AF: 0.222 AC: 338 AN: 1525

Alfa AF: 0.237 Hom.: 7971

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.54
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1905182; hg19: chrX-82595918;