X-66386519-T-A

Variant names:

• chrX-66386519-T-A
• rs1379146

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 (21392 hom., 23475 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	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: 79860 AN: 109563 Hom.: 21396 Cov.: 22

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.802

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.761

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: 79887 AN: 109618 Hom.: 21392 Cov.: 22 AF XY: 0.734 AC XY: 23475 AN XY: 31964

African (AFR) AF: 0.492 AC: 14848 AN: 30154

American (AMR) AF: 0.858 AC: 8782 AN: 10240

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 2398 AN: 2614

East Asian (EAS) AF: 0.997 AC: 3439 AN: 3448

South Asian (SAS) AF: 0.900 AC: 2233 AN: 2482

European-Finnish (FIN) AF: 0.747 AC: 4294 AN: 5747

Middle Eastern (MID) AF: 0.796 AC: 172 AN: 216

European-Non Finnish (NFE) AF: 0.799 AC: 41993 AN: 52547

Other (OTH) AF: 0.762 AC: 1139 AN: 1494

Alfa AF: 0.756 Hom.: 6247

Bravo AF: 0.728

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1379146; hg19: chrX-65606361;