X-858939-T-C

Variant names:

• chrX-858939-T-C
• rs35352127

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;