rs1635217

Variant names:

• chrX-3302702-A-G
• rs1635217

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 (15285 hom., 20674 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• 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=-0.97).

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: 69145 AN: 111055 Hom.: 15298 Cov.: 23

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.639

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: 0.622 AC: 69142 AN: 111111 Hom.: 15285 Cov.: 23 AF XY: 0.620 AC XY: 20674 AN XY: 33355

African (AFR) AF: 0.527 AC: 16132 AN: 30605

American (AMR) AF: 0.635 AC: 6667 AN: 10493

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 1758 AN: 2634

East Asian (EAS) AF: 0.732 AC: 2566 AN: 3505

South Asian (SAS) AF: 0.650 AC: 1722 AN: 2650

European-Finnish (FIN) AF: 0.688 AC: 4031 AN: 5860

Middle Eastern (MID) AF: 0.682 AC: 144 AN: 211

European-Non Finnish (NFE) AF: 0.655 AC: 34684 AN: 52962

Other (OTH) AF: 0.631 AC: 954 AN: 1513

Alfa AF: 0.643 Hom.: 6103

Bravo AF: 0.616

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.46
PhyloP100		-0.92

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: rs1635217;

hg19: chrX-3220743;