X-15189904-C-T

Variant names:

• chrX-15189904-C-T
• rs1993969

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.55 (11895 hom., 17878 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.548 AC: 60406 AN: 110205 Hom.: 11897 Cov.: 23

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.565

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.548 AC: 60436 AN: 110255 Hom.: 11895 Cov.: 23 AF XY: 0.549 AC XY: 17878 AN XY: 32573

African (AFR) AF: 0.569 AC: 17278 AN: 30345

American (AMR) AF: 0.630 AC: 6527 AN: 10358

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 1567 AN: 2615

East Asian (EAS) AF: 0.862 AC: 3027 AN: 3513

South Asian (SAS) AF: 0.567 AC: 1478 AN: 2605

European-Finnish (FIN) AF: 0.464 AC: 2698 AN: 5812

Middle Eastern (MID) AF: 0.529 AC: 110 AN: 208

European-Non Finnish (NFE) AF: 0.508 AC: 26747 AN: 52623

Other (OTH) AF: 0.570 AC: 853 AN: 1497

Alfa AF: 0.516 Hom.: 3728

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.28
PhyloP100		-0.60

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1993969;

hg19: chrX-15208026;