rs2369646

Variant names:

• chrX-87215053-C-T
• rs2369646

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 0.262 in 109,556 control chromosomes in the GnomAD database, including 3,013 homozygotes. There are 8,343 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 (3013 hom., 8343 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.262 AC: 28684 AN: 109506 Hom.: 3008 Cov.: 22

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.262 AC: 28707 AN: 109556 Hom.: 3013 Cov.: 22 AF XY: 0.260 AC XY: 8343 AN XY: 32140

African (AFR) AF: 0.354 AC: 10745 AN: 30312

American (AMR) AF: 0.380 AC: 3892 AN: 10249

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 578 AN: 2611

East Asian (EAS) AF: 0.0602 AC: 210 AN: 3490

South Asian (SAS) AF: 0.203 AC: 526 AN: 2593

European-Finnish (FIN) AF: 0.221 AC: 1266 AN: 5719

Middle Eastern (MID) AF: 0.214 AC: 45 AN: 210

European-Non Finnish (NFE) AF: 0.208 AC: 10841 AN: 52200

Other (OTH) AF: 0.249 AC: 372 AN: 1492

Alfa AF: 0.231 Hom.: 22468

Bravo AF: 0.282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.58
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2369646; hg19: chrX-86470056;