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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs7051285; hg19: chrX-70426978;