chrX-117852908-G-T

Variant names:

• chrX-117852908-G-T
• rs883955

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 0.316 in 111,357 control chromosomes in the GnomAD database, including 4,157 homozygotes. There are 10,292 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 0.32 (4157 hom., 10292 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.316 AC: 35193 AN: 111301 Hom.: 4153 Cov.: 23

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.316 AC: 35232 AN: 111357 Hom.: 4157 Cov.: 23 AF XY: 0.306 AC XY: 10292 AN XY: 33605

African (AFR) AF: 0.373 AC: 11437 AN: 30665

American (AMR) AF: 0.196 AC: 2062 AN: 10547

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 979 AN: 2632

East Asian (EAS) AF: 0.276 AC: 968 AN: 3507

South Asian (SAS) AF: 0.259 AC: 701 AN: 2709

European-Finnish (FIN) AF: 0.281 AC: 1673 AN: 5947

Middle Eastern (MID) AF: 0.373 AC: 81 AN: 217

European-Non Finnish (NFE) AF: 0.316 AC: 16738 AN: 52936

Other (OTH) AF: 0.309 AC: 470 AN: 1523

Alfa AF: 0.292 Hom.: 8068

Bravo AF: 0.315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs883955; hg19: chrX-116986871;