X-861169-C-T

Variant names:

• chrX-861169-C-T
• rs35614363

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 0.0354 in 149,018 control chromosomes in the GnomAD database, including 470 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 0.035 (470 hom., 2600 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0573 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5287 AN: 148894 Hom.: 469 Cov.: 29

Gnomad AFR AF: 0.00584

Gnomad AMI AF: 0.0767

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000789

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.0389

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

GnomAD4 genome AF: 0.0354 AC: 5282 AN: 149018 Hom.: 470 Cov.: 29 AF XY: 0.0358 AC XY: 2600 AN XY: 72558

African (AFR) AF: 0.00582 AC: 239 AN: 41056

American (AMR) AF: 0.0342 AC: 507 AN: 14806

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 394 AN: 3436

East Asian (EAS) AF: 0.000791 AC: 4 AN: 5058

South Asian (SAS) AF: 0.0633 AC: 295 AN: 4662

European-Finnish (FIN) AF: 0.0494 AC: 502 AN: 10152

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0476 AC: 3173 AN: 66628

Other (OTH) AF: 0.0380 AC: 78 AN: 2054

Bravo AF: 0.0314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.81
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs35614363; hg19: chrX-821904;