chrX-66866114-G-A

Variant names:

• chrX-66866114-G-A
• rs1041668

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 0.65 (20514 hom., 21885 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.655 AC: 72394 AN: 110591 Hom.: 20522 Cov.: 23

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.754

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.707

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: 0.654 AC: 72384 AN: 110644 Hom.: 20514 Cov.: 23 AF XY: 0.665 AC XY: 21885 AN XY: 32892

African (AFR) AF: 0.138 AC: 4232 AN: 30613

American (AMR) AF: 0.832 AC: 8588 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 2446 AN: 2635

East Asian (EAS) AF: 0.998 AC: 3472 AN: 3479

South Asian (SAS) AF: 0.921 AC: 2379 AN: 2583

European-Finnish (FIN) AF: 0.821 AC: 4766 AN: 5805

Middle Eastern (MID) AF: 0.753 AC: 162 AN: 215

European-Non Finnish (NFE) AF: 0.846 AC: 44669 AN: 52813

Other (OTH) AF: 0.710 AC: 1070 AN: 1507

Alfa AF: 0.795 Hom.: 50237

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.44
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1041668; hg19: chrX-66085956; COSMIC: COSV68315964;