X-71206075-C-T

Variant names:

• chrX-71206075-C-T
• rs35328964

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 (15000 hom., 17163 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• 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=-1.01).

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: 0.593 AC: 63447 AN: 106924 Hom.: 14991 Cov.: 20

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.624

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: 0.594 AC: 63506 AN: 106974 Hom.: 15000 Cov.: 20 AF XY: 0.582 AC XY: 17163 AN XY: 29514

African (AFR) AF: 0.823 AC: 24079 AN: 29263

American (AMR) AF: 0.625 AC: 6122 AN: 9788

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1759 AN: 2597

East Asian (EAS) AF: 0.745 AC: 2515 AN: 3375

South Asian (SAS) AF: 0.590 AC: 1437 AN: 2437

European-Finnish (FIN) AF: 0.378 AC: 1968 AN: 5210

Middle Eastern (MID) AF: 0.675 AC: 141 AN: 209

European-Non Finnish (NFE) AF: 0.464 AC: 24122 AN: 51969

Other (OTH) AF: 0.629 AC: 919 AN: 1460

Alfa AF: 0.525 Hom.: 3741

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	0.15
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs35328964; hg19: chrX-70425925;