X-121445819-C-G

Variant names:

• chrX-121445819-C-G
• rs4825770

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 0.81 (25600 hom., 27369 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.813 AC: 90284 AN: 110990 Hom.: 25598 Cov.: 23

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.808

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: 0.814 AC: 90332 AN: 111040 Hom.: 25600 Cov.: 23 AF XY: 0.823 AC XY: 27369 AN XY: 33252

African (AFR) AF: 0.797 AC: 24400 AN: 30634

American (AMR) AF: 0.881 AC: 9165 AN: 10399

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 1827 AN: 2638

East Asian (EAS) AF: 0.999 AC: 3526 AN: 3531

South Asian (SAS) AF: 0.935 AC: 2453 AN: 2624

European-Finnish (FIN) AF: 0.830 AC: 4867 AN: 5866

Middle Eastern (MID) AF: 0.612 AC: 131 AN: 214

European-Non Finnish (NFE) AF: 0.795 AC: 42099 AN: 52925

Other (OTH) AF: 0.810 AC: 1237 AN: 1527

Alfa AF: 0.788 Hom.: 6250

Bravo AF: 0.817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.72
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4825770; hg19: chrX-120579673;