X-47826606-T-C

Variant names:

• chrX-47826606-T-C
• rs1207480

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 0.59 (13911 hom., 18569 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.587 AC: 64405 AN: 109730 Hom.: 13909 Cov.: 22

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.593

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: 0.587 AC: 64451 AN: 109781 Hom.: 13911 Cov.: 22 AF XY: 0.578 AC XY: 18569 AN XY: 32115

African (AFR) AF: 0.693 AC: 20888 AN: 30149

American (AMR) AF: 0.642 AC: 6571 AN: 10237

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1444 AN: 2626

East Asian (EAS) AF: 0.781 AC: 2687 AN: 3441

South Asian (SAS) AF: 0.530 AC: 1377 AN: 2600

European-Finnish (FIN) AF: 0.440 AC: 2510 AN: 5704

Middle Eastern (MID) AF: 0.678 AC: 145 AN: 214

European-Non Finnish (NFE) AF: 0.525 AC: 27626 AN: 52634

Other (OTH) AF: 0.598 AC: 900 AN: 1505

Alfa AF: 0.562 Hom.: 12054

Bravo AF: 0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.84
PhyloP100		0.057

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: rs1207480;

hg19: chrX-47686005;