X-843365-G-C

Position:

• chrX-843365-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 0.263 in 151,508 control chromosomes in the GnomAD database, including 5,892 homozygotes. There are 19,511 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 0.26 (5892 hom., 19511 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.264 AC: 39915 AN: 151390 Hom.: 5893 Cov.: 31 AF XY: 0.264 AC XY: 19499 AN XY: 73880

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0211

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.263 AC: 39916 AN: 151508 Hom.: 5892 Cov.: 31 AF XY: 0.264 AC XY: 19511 AN XY: 74008

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.0211

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.249

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946324; hg19: chrX-804100;