X-66052274-A-G

Variant names:

• chrX-66052274-A-G
• rs670546

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 0.79 (24942 hom., 26315 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.791 AC: 87624 AN: 110724 Hom.: 24949 Cov.: 23

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.829

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: 0.791 AC: 87633 AN: 110774 Hom.: 24942 Cov.: 23 AF XY: 0.797 AC XY: 26315 AN XY: 33006

African (AFR) AF: 0.574 AC: 17458 AN: 30434

American (AMR) AF: 0.825 AC: 8623 AN: 10454

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 2366 AN: 2634

East Asian (EAS) AF: 0.999 AC: 3543 AN: 3545

South Asian (SAS) AF: 0.918 AC: 2375 AN: 2587

European-Finnish (FIN) AF: 0.880 AC: 5130 AN: 5830

Middle Eastern (MID) AF: 0.852 AC: 184 AN: 216

European-Non Finnish (NFE) AF: 0.872 AC: 46125 AN: 52899

Other (OTH) AF: 0.829 AC: 1244 AN: 1500

Alfa AF: 0.839 Hom.: 94086

Bravo AF: 0.779

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs670546; hg19: chrX-65272116;