chrX-71206319-T-C

Variant names:

• chrX-71206319-T-C
• rs34030408

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 0.60 (15033 hom., 18544 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-1.02).

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: 0.599 AC: 64900 AN: 108315 Hom.: 15024 Cov.: 21

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.634

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: 0.599 AC: 64960 AN: 108362 Hom.: 15033 Cov.: 21 AF XY: 0.600 AC XY: 18544 AN XY: 30898

African (AFR) AF: 0.826 AC: 24675 AN: 29881

American (AMR) AF: 0.632 AC: 6403 AN: 10126

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 1772 AN: 2614

East Asian (EAS) AF: 0.750 AC: 2549 AN: 3399

South Asian (SAS) AF: 0.605 AC: 1533 AN: 2535

European-Finnish (FIN) AF: 0.403 AC: 2158 AN: 5352

Middle Eastern (MID) AF: 0.689 AC: 144 AN: 209

European-Non Finnish (NFE) AF: 0.467 AC: 24353 AN: 52125

Other (OTH) AF: 0.639 AC: 943 AN: 1475

Alfa AF: 0.543 Hom.: 4094

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs34030408; hg19: chrX-70426169;