chrX-66386851-T-A

Variant names:

• chrX-66386851-T-A
• rs5965182

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).

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: 0.729 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 v4.3

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;