rs5965182

Variant names:

• chrX-66386851-T-A
• rs5965182

Your query was ambiguous. Multiple possible variants found:

• chrX-66386851-T-A
• chrX-66386851-T-C
• chrX-66386851-T-G

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 0.73 (21397 hom., 23505 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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: 0.729 AC: 79885 AN: 109620 Hom.: 21401 Cov.: 22

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.758

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: 0.729 AC: 79915 AN: 109676 Hom.: 21397 Cov.: 22 AF XY: 0.734 AC XY: 23505 AN XY: 32034

African (AFR) AF: 0.492 AC: 14854 AN: 30187

American (AMR) AF: 0.857 AC: 8760 AN: 10224

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 2407 AN: 2623

East Asian (EAS) AF: 0.997 AC: 3443 AN: 3453

South Asian (SAS) AF: 0.902 AC: 2272 AN: 2520

European-Finnish (FIN) AF: 0.751 AC: 4332 AN: 5770

Middle Eastern (MID) AF: 0.792 AC: 171 AN: 216

European-Non Finnish (NFE) AF: 0.799 AC: 41947 AN: 52508

Other (OTH) AF: 0.760 AC: 1138 AN: 1497

Alfa AF: 0.802 Hom.: 30096

Bravo AF: 0.728

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5965182; hg19: chrX-65606693;