X-39675542-C-G

Variant names:

• chrX-39675542-C-G
• rs206034

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 0.357 in 111,388 control chromosomes in the GnomAD database, including 5,172 homozygotes. There are 11,937 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 0.36 (5172 hom., 11937 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.357 AC: 39712 AN: 111334 Hom.: 5170 Cov.: 23 AF XY: 0.355 AC XY: 11926 AN XY: 33552

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.390

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.357 AC: 39729 AN: 111388 Hom.: 5172 Cov.: 23 AF XY: 0.355 AC XY: 11937 AN XY: 33616

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.403

Alfa AF: 0.350 Hom.: 2500

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.092
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206034; hg19: chrX-39534796;