rs1635216

Variant names:

• chrX-3302678-G-A
• rs1635216

Your query was ambiguous. Multiple possible variants found:

• chrX-3302678-G-A
• chrX-3302678-G-C
• chrX-3302678-G-T

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 0.62 (15282 hom., 20609 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• 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=-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: 0.623 AC: 69075 AN: 110874 Hom.: 15295 Cov.: 24

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.637

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: 0.623 AC: 69071 AN: 110928 Hom.: 15282 Cov.: 24 AF XY: 0.621 AC XY: 20609 AN XY: 33188

African (AFR) AF: 0.527 AC: 16058 AN: 30465

American (AMR) AF: 0.636 AC: 6666 AN: 10476

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 1758 AN: 2631

East Asian (EAS) AF: 0.733 AC: 2562 AN: 3494

South Asian (SAS) AF: 0.651 AC: 1730 AN: 2659

European-Finnish (FIN) AF: 0.688 AC: 4015 AN: 5833

Middle Eastern (MID) AF: 0.687 AC: 147 AN: 214

European-Non Finnish (NFE) AF: 0.655 AC: 34704 AN: 52971

Other (OTH) AF: 0.629 AC: 948 AN: 1507

Alfa AF: 0.644 Hom.: 6109

Bravo AF: 0.616

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.32
PhyloP100		-0.63

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: rs1635216;

hg19: chrX-3220719;