X-150277818-G-A

Variant names:

• chrX-150277818-G-A
• rs9723770

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 0.96 (35835 hom., 31179 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 1 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: 0.959 AC: 105657 AN: 110194 Hom.: 35842 Cov.: 22

Gnomad AFR AF: 0.859

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.964

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: 0.959 AC: 105705 AN: 110251 Hom.: 35835 Cov.: 22 AF XY: 0.961 AC XY: 31179 AN XY: 32455

African (AFR) AF: 0.859 AC: 25985 AN: 30245

American (AMR) AF: 0.979 AC: 10132 AN: 10347

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2636 AN: 2636

East Asian (EAS) AF: 1.00 AC: 3514 AN: 3514

South Asian (SAS) AF: 1.00 AC: 2438 AN: 2439

European-Finnish (FIN) AF: 1.00 AC: 5871 AN: 5871

Middle Eastern (MID) AF: 0.986 AC: 214 AN: 217

European-Non Finnish (NFE) AF: 1.00 AC: 52778 AN: 52792

Other (OTH) AF: 0.965 AC: 1455 AN: 1508

Alfa AF: 0.969 Hom.: 6159

Bravo AF: 0.950

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.87
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs9723770; hg19: chrX-149446036;