chrX-79687224-C-A

Variant names:

• chrX-79687224-C-A
• rs1353456

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 0.63 (17218 hom., 20833 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• 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=-0.8).

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: 0.627 AC: 69417 AN: 110686 Hom.: 17228 Cov.: 24

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.672

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: 0.627 AC: 69419 AN: 110738 Hom.: 17218 Cov.: 24 AF XY: 0.631 AC XY: 20833 AN XY: 33002

African (AFR) AF: 0.283 AC: 8648 AN: 30546

American (AMR) AF: 0.569 AC: 5914 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2181 AN: 2640

East Asian (EAS) AF: 0.627 AC: 2175 AN: 3470

South Asian (SAS) AF: 0.860 AC: 2281 AN: 2652

European-Finnish (FIN) AF: 0.762 AC: 4450 AN: 5838

Middle Eastern (MID) AF: 0.817 AC: 174 AN: 213

European-Non Finnish (NFE) AF: 0.795 AC: 41996 AN: 52821

Other (OTH) AF: 0.673 AC: 1000 AN: 1486

Alfa AF: 0.721 Hom.: 34164

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1353456; hg19: chrX-78942721;