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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs1635216; hg19: chrX-3220719;