rs3027869

chrX-153946086-G-AchrX-153946086-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 0.212 in 110,849 control chromosomes in the GnomAD database, including 2,596 homozygotes. There are 7,315 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 0.21 (2596 hom., 7315 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.212 AC: 23484 AN: 110795 Hom.: 2590 Cov.: 24 AF XY: 0.221 AC XY: 7308 AN XY: 33045

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.212 AC: 23493 AN: 110849 Hom.: 2596 Cov.: 24 AF XY: 0.221 AC XY: 7315 AN XY: 33109

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.270

Alfa AF: 0.196 Hom.: 1181

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.1
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3027869; hg19: chrX-153211538; COSMIC: COSV60078671;