X-81007519-T-C

Variant names:

• chrX-81007519-T-C
• rs1166638

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 0.65 (17672 hom., 21454 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• 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=-0.91).

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: 0.649 AC: 71737 AN: 110550 Hom.: 17681 Cov.: 23

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.779

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.654

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: 0.649 AC: 71761 AN: 110602 Hom.: 17672 Cov.: 23 AF XY: 0.653 AC XY: 21454 AN XY: 32858

African (AFR) AF: 0.353 AC: 10777 AN: 30522

American (AMR) AF: 0.696 AC: 7195 AN: 10338

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2046 AN: 2636

East Asian (EAS) AF: 0.820 AC: 2872 AN: 3504

South Asian (SAS) AF: 0.699 AC: 1835 AN: 2625

European-Finnish (FIN) AF: 0.771 AC: 4458 AN: 5785

Middle Eastern (MID) AF: 0.780 AC: 167 AN: 214

European-Non Finnish (NFE) AF: 0.773 AC: 40783 AN: 52782

Other (OTH) AF: 0.656 AC: 994 AN: 1515

Alfa AF: 0.682 Hom.: 4460

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.91
PhyloP100		-1.4

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: rs1166638;

hg19: chrX-80263018;