X-3202739-T-C

Variant names:

• chrX-3202739-T-C
• rs7058025

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.336 AC: 37122 AN: 110466 Hom.: 4616 Cov.: 22

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

African (AFR) AF: 0.277 AC: 8429 AN: 30463

American (AMR) AF: 0.398 AC: 4099 AN: 10305

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 879 AN: 2632

East Asian (EAS) AF: 0.540 AC: 1876 AN: 3473

South Asian (SAS) AF: 0.233 AC: 609 AN: 2609

European-Finnish (FIN) AF: 0.350 AC: 2043 AN: 5841

Middle Eastern (MID) AF: 0.392 AC: 85 AN: 217

European-Non Finnish (NFE) AF: 0.349 AC: 18440 AN: 52814

Other (OTH) AF: 0.333 AC: 497 AN: 1491

Alfa AF: 0.350 Hom.: 37612

Bravo AF: 0.348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs7058025; hg19: chrX-3120780;