rs4827678

Variant names:

• chrX-145995800-G-A
• rs4827678

Your query was ambiguous. Multiple possible variants found:

• chrX-145995800-G-A
• chrX-145995800-G-C

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 0.61 (14897 hom., 19231 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.608 AC: 66730 AN: 109735 Hom.: 14889 Cov.: 22

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.583

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: 0.608 AC: 66773 AN: 109779 Hom.: 14897 Cov.: 22 AF XY: 0.599 AC XY: 19231 AN XY: 32103

African (AFR) AF: 0.745 AC: 22428 AN: 30113

American (AMR) AF: 0.553 AC: 5669 AN: 10259

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1164 AN: 2625

East Asian (EAS) AF: 0.587 AC: 2017 AN: 3439

South Asian (SAS) AF: 0.637 AC: 1614 AN: 2532

European-Finnish (FIN) AF: 0.555 AC: 3185 AN: 5735

Middle Eastern (MID) AF: 0.574 AC: 120 AN: 209

European-Non Finnish (NFE) AF: 0.558 AC: 29422 AN: 52702

Other (OTH) AF: 0.584 AC: 874 AN: 1496

Alfa AF: 0.577 Hom.: 71809

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.48
PhyloP100		-2.0

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: rs4827678;

hg19: chrX-145077318;