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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs12559781; hg19: chrX-4215952;