X-67120595-A-G

Variant names:

• chrX-67120595-A-G
• rs925391

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 (20379 hom., 21234 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• 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=-0.87).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.652 AC: 71574 AN: 109793 Hom.: 20388 Cov.: 22

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.700

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: 0.652 AC: 71566 AN: 109846 Hom.: 20379 Cov.: 22 AF XY: 0.661 AC XY: 21234 AN XY: 32118

African (AFR) AF: 0.138 AC: 4216 AN: 30501

American (AMR) AF: 0.827 AC: 8438 AN: 10207

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2409 AN: 2622

East Asian (EAS) AF: 0.999 AC: 3419 AN: 3424

South Asian (SAS) AF: 0.920 AC: 2288 AN: 2488

European-Finnish (FIN) AF: 0.828 AC: 4675 AN: 5645

Middle Eastern (MID) AF: 0.751 AC: 160 AN: 213

European-Non Finnish (NFE) AF: 0.843 AC: 44334 AN: 52602

Other (OTH) AF: 0.702 AC: 1032 AN: 1471

Alfa AF: 0.762 Hom.: 61636

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs925391; hg19: chrX-66340437;