X-71319639-C-T

Variant names:

• chrX-71319639-C-T
• rs12845815

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 0.75 (21520 hom., 13599 hem., cov: 15)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 0 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: 0.754 AC: 69554 AN: 92241 Hom.: 21526 Cov.: 15

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.788

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: 0.754 AC: 69548 AN: 92249 Hom.: 21520 Cov.: 15 AF XY: 0.735 AC XY: 13599 AN XY: 18505

African (AFR) AF: 0.604 AC: 15316 AN: 25368

American (AMR) AF: 0.836 AC: 6730 AN: 8054

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 1984 AN: 2374

East Asian (EAS) AF: 0.656 AC: 1752 AN: 2672

South Asian (SAS) AF: 0.611 AC: 1032 AN: 1689

European-Finnish (FIN) AF: 0.839 AC: 2551 AN: 3040

Middle Eastern (MID) AF: 0.882 AC: 149 AN: 169

European-Non Finnish (NFE) AF: 0.819 AC: 38580 AN: 47092

Other (OTH) AF: 0.788 AC: 958 AN: 1216

Alfa AF: 0.602 Hom.: 1925

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.57
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12845815;

hg19: chrX-70539489;