X-71209374-C-G

Variant names:

• chrX-71209374-C-G
• rs6525481

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 0.59 (14933 hom., 19391 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• 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=-1.0).

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: 0.594 AC: 65652 AN: 110482 Hom.: 14924 Cov.: 23

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.618

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: 0.595 AC: 65715 AN: 110536 Hom.: 14933 Cov.: 23 AF XY: 0.591 AC XY: 19391 AN XY: 32808

African (AFR) AF: 0.821 AC: 24979 AN: 30412

American (AMR) AF: 0.625 AC: 6431 AN: 10290

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 1790 AN: 2629

East Asian (EAS) AF: 0.748 AC: 2609 AN: 3486

South Asian (SAS) AF: 0.587 AC: 1549 AN: 2640

European-Finnish (FIN) AF: 0.403 AC: 2369 AN: 5883

Middle Eastern (MID) AF: 0.671 AC: 145 AN: 216

European-Non Finnish (NFE) AF: 0.463 AC: 24463 AN: 52809

Other (OTH) AF: 0.624 AC: 936 AN: 1499

Alfa AF: 0.541 Hom.: 4070

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.52
PhyloP100		-0.43

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: rs6525481; hg19: chrX-70429224;