rs1905182

Positions:

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

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 0.209 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.210 AC: 23286 AN: 111122 Hom.: 2025 Cov.: 23 AF XY: 0.214 AC XY: 7114 AN XY: 33320

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

Gnomad4 AFR AF: 0.0732

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.222

Alfa AF: 0.251 Hom.: 5901

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
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: rs1905182; hg19: chrX-82595918;