chrX-858939-T-C

Position:

• chrX-858939-T-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 0.0326 in 151,926 control chromosomes in the GnomAD database, including 184 homozygotes. There are 2,600 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 0.033 (184 hom., 2600 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0324 AC: 4918 AN: 151806 Hom.: 174 Cov.: 31 AF XY: 0.0349 AC XY: 2588 AN XY: 74128

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0326 AC: 4957 AN: 151926 Hom.: 184 Cov.: 31 AF XY: 0.0350 AC XY: 2600 AN XY: 74258

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.0834

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35352127; hg19: chrX-819674;