X-116232733-G-T

Variant names:

• chrX-116232733-G-T
• rs5952206

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 0.445 in 110,327 control chromosomes in the GnomAD database, including 8,364 homozygotes. There are 14,015 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 0.45 (8364 hom., 14015 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 0.445 AC: 49079 AN: 110277 Hom.: 8365 Cov.: 22

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.498

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.445 AC: 49103 AN: 110327 Hom.: 8364 Cov.: 22 AF XY: 0.430 AC XY: 14015 AN XY: 32595

African (AFR) AF: 0.564 AC: 17067 AN: 30265

American (AMR) AF: 0.287 AC: 2992 AN: 10426

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 964 AN: 2620

East Asian (EAS) AF: 0.225 AC: 788 AN: 3506

South Asian (SAS) AF: 0.421 AC: 1074 AN: 2554

European-Finnish (FIN) AF: 0.429 AC: 2476 AN: 5777

Middle Eastern (MID) AF: 0.495 AC: 106 AN: 214

European-Non Finnish (NFE) AF: 0.431 AC: 22726 AN: 52772

Other (OTH) AF: 0.417 AC: 633 AN: 1519

Alfa AF: 0.434 Hom.: 23113

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.62
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs5952206; hg19: chrX-115363988;