X-15624289-G-C

Position:

• chrX-15624289-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 0.3 in 110,868 control chromosomes in the GnomAD database, including 3,623 homozygotes. There are 9,849 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 0.30 (3623 hom., 9849 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 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: 0.300 AC: 33215 AN: 110815 Hom.: 3619 Cov.: 23 AF XY: 0.297 AC XY: 9841 AN XY: 33085

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.300 AC: 33236 AN: 110868 Hom.: 3623 Cov.: 23 AF XY: 0.297 AC XY: 9849 AN XY: 33148

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.317

Alfa AF: 0.105 Hom.: 455

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356037; hg19: chrX-15642412;