rs5969181

chrX-87368646-G-AchrX-87368646-G-C

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 0.363 in 109,889 control chromosomes in the GnomAD database, including 5,355 homozygotes. There are 11,403 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 0.36 (5355 hom., 11403 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.363 AC: 39843 AN: 109842 Hom.: 5356 Cov.: 22 AF XY: 0.354 AC XY: 11395 AN XY: 32164

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.363 AC: 39849 AN: 109889 Hom.: 5355 Cov.: 22 AF XY: 0.354 AC XY: 11403 AN XY: 32221

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.344

Alfa AF: 0.358 Hom.: 20615

Bravo AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5969181; hg19: chrX-86623649;