X-87412105-G-A

Variant names:

• chrX-87412105-G-A
• rs959060

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 0.84 (27538 hom., 26913 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• 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=-1.04).

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: 0.840 AC: 92085 AN: 109602 Hom.: 27539 Cov.: 22

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.842

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: 0.840 AC: 92136 AN: 109649 Hom.: 27538 Cov.: 22 AF XY: 0.844 AC XY: 26913 AN XY: 31873

African (AFR) AF: 0.936 AC: 28321 AN: 30263

American (AMR) AF: 0.874 AC: 8907 AN: 10193

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2072 AN: 2619

East Asian (EAS) AF: 0.915 AC: 3196 AN: 3493

South Asian (SAS) AF: 0.793 AC: 2040 AN: 2571

European-Finnish (FIN) AF: 0.842 AC: 4696 AN: 5574

Middle Eastern (MID) AF: 0.836 AC: 179 AN: 214

European-Non Finnish (NFE) AF: 0.780 AC: 40974 AN: 52558

Other (OTH) AF: 0.846 AC: 1272 AN: 1504

Alfa AF: 0.796 Hom.: 42261

Bravo AF: 0.849

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.21
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs959060; hg19: chrX-86667108;