rs210453

Variant names:

• chrX-83161825-A-G
• rs210453

Your query was ambiguous. Multiple possible variants found:

• chrX-83161825-A-G
• chrX-83161825-A-T

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 0.259 in 110,489 control chromosomes in the GnomAD database, including 3,266 homozygotes. There are 8,171 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 0.26 (3266 hom., 8171 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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: 0.259 AC: 28554 AN: 110441 Hom.: 3262 Cov.: 22

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.0966

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.251

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.259 AC: 28585 AN: 110489 Hom.: 3266 Cov.: 22 AF XY: 0.249 AC XY: 8171 AN XY: 32787

African (AFR) AF: 0.433 AC: 13078 AN: 30232

American (AMR) AF: 0.316 AC: 3294 AN: 10426

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 327 AN: 2631

East Asian (EAS) AF: 0.194 AC: 667 AN: 3438

South Asian (SAS) AF: 0.181 AC: 474 AN: 2612

European-Finnish (FIN) AF: 0.180 AC: 1060 AN: 5896

Middle Eastern (MID) AF: 0.224 AC: 48 AN: 214

European-Non Finnish (NFE) AF: 0.174 AC: 9183 AN: 52865

Other (OTH) AF: 0.260 AC: 388 AN: 1492

Alfa AF: 0.215 Hom.: 6017

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs210453; hg19: chrX-82416833;