rs12559781

Variant names:

• chrX-4297911-T-C
• rs12559781

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 0.53 (11921 hom., 16690 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• 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=-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: 0.531 AC: 58583 AN: 110308 Hom.: 11917 Cov.: 22

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.530

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.519

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: 0.531 AC: 58627 AN: 110364 Hom.: 11921 Cov.: 22 AF XY: 0.510 AC XY: 16690 AN XY: 32722

African (AFR) AF: 0.693 AC: 21042 AN: 30383

American (AMR) AF: 0.386 AC: 4008 AN: 10372

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1381 AN: 2630

East Asian (EAS) AF: 0.186 AC: 645 AN: 3471

South Asian (SAS) AF: 0.376 AC: 994 AN: 2641

European-Finnish (FIN) AF: 0.447 AC: 2627 AN: 5872

Middle Eastern (MID) AF: 0.538 AC: 114 AN: 212

European-Non Finnish (NFE) AF: 0.507 AC: 26693 AN: 52619

Other (OTH) AF: 0.512 AC: 763 AN: 1491

Alfa AF: 0.503 Hom.: 21190

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.42
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: rs12559781;

hg19: chrX-4215952;