X-3202739-T-C

Variant names:

• chrX-3202739-T-C
• rs7058025

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 0.336 in 110,518 control chromosomes in the GnomAD database, including 4,610 homozygotes. There are 10,802 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 0.34 (4610 hom., 10802 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

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 (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.336 AC: 37122 AN: 110466 Hom.: 4616 Cov.: 22 AF XY: 0.330 AC XY: 10793 AN XY: 32734

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.336 AC: 37116 AN: 110518 Hom.: 4610 Cov.: 22 AF XY: 0.329 AC XY: 10802 AN XY: 32796

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.333

Alfa AF: 0.350 Hom.: 30999

Bravo AF: 0.348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7058025; hg19: chrX-3120780;