X-76185904-G-A

Variant names:

• chrX-76185904-G-A
• rs2214607

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 0.75 (22603 hom., 24276 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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: 0.751 AC: 82839 AN: 110262 Hom.: 22610 Cov.: 23

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.757

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: 0.751 AC: 82889 AN: 110316 Hom.: 22603 Cov.: 23 AF XY: 0.746 AC XY: 24276 AN XY: 32550

African (AFR) AF: 0.704 AC: 21340 AN: 30315

American (AMR) AF: 0.699 AC: 7208 AN: 10314

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2200 AN: 2620

East Asian (EAS) AF: 0.221 AC: 777 AN: 3522

South Asian (SAS) AF: 0.667 AC: 1725 AN: 2588

European-Finnish (FIN) AF: 0.814 AC: 4704 AN: 5780

Middle Eastern (MID) AF: 0.863 AC: 183 AN: 212

European-Non Finnish (NFE) AF: 0.815 AC: 43032 AN: 52788

Other (OTH) AF: 0.750 AC: 1125 AN: 1499

Alfa AF: 0.789 Hom.: 101590

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs2214607; hg19: chrX-75405739;