X-71207128-A-T

Variant names:

• chrX-71207128-A-T
• rs7051285

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 (15035 hom., 17401 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• 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=-0.88).

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: 0.595 AC: 63769 AN: 107124 Hom.: 15026 Cov.: 20

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.623

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: 63804 AN: 107146 Hom.: 15035 Cov.: 20 AF XY: 0.587 AC XY: 17401 AN XY: 29632

African (AFR) AF: 0.824 AC: 24341 AN: 29525

American (AMR) AF: 0.627 AC: 6216 AN: 9906

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 1748 AN: 2591

East Asian (EAS) AF: 0.749 AC: 2461 AN: 3287

South Asian (SAS) AF: 0.591 AC: 1411 AN: 2388

European-Finnish (FIN) AF: 0.394 AC: 2062 AN: 5240

Middle Eastern (MID) AF: 0.677 AC: 136 AN: 201

European-Non Finnish (NFE) AF: 0.464 AC: 24081 AN: 51902

Other (OTH) AF: 0.628 AC: 911 AN: 1450

Alfa AF: 0.518 Hom.: 4120

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.81
PhyloP100		0.24

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: rs7051285;

hg19: chrX-70426978;