X-71207339-A-G

Variant names:

• chrX-71207339-A-G
• rs7878264

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 (14906 hom., 15042 hem., cov: 18)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• 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=-1.03).

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: 0.596 AC: 61028 AN: 102472 Hom.: 14897 Cov.: 18

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.631

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: 0.596 AC: 61071 AN: 102499 Hom.: 14906 Cov.: 18 AF XY: 0.587 AC XY: 15042 AN XY: 25627

African (AFR) AF: 0.824 AC: 23298 AN: 28271

American (AMR) AF: 0.629 AC: 5938 AN: 9437

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1729 AN: 2554

East Asian (EAS) AF: 0.752 AC: 2241 AN: 2982

South Asian (SAS) AF: 0.607 AC: 1183 AN: 1950

European-Finnish (FIN) AF: 0.393 AC: 1817 AN: 4625

Middle Eastern (MID) AF: 0.680 AC: 136 AN: 200

European-Non Finnish (NFE) AF: 0.464 AC: 23408 AN: 50437

Other (OTH) AF: 0.637 AC: 901 AN: 1415

Alfa AF: 0.543 Hom.: 4090

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	2.7
DANN	Benign	0.40
PhyloP100		-1.2

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: rs7878264; hg19: chrX-70427189;