X-83190918-T-G

Variant names:

• chrX-83190918-T-G
• rs210465

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 0.74 (21949 hom., 24071 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.738 AC: 81081 AN: 109930 Hom.: 21942 Cov.: 22

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.735

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: 0.738 AC: 81140 AN: 109976 Hom.: 21949 Cov.: 22 AF XY: 0.746 AC XY: 24071 AN XY: 32264

African (AFR) AF: 0.944 AC: 28614 AN: 30309

American (AMR) AF: 0.744 AC: 7667 AN: 10304

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 1628 AN: 2629

East Asian (EAS) AF: 0.995 AC: 3473 AN: 3490

South Asian (SAS) AF: 0.768 AC: 1978 AN: 2577

European-Finnish (FIN) AF: 0.736 AC: 4121 AN: 5600

Middle Eastern (MID) AF: 0.692 AC: 148 AN: 214

European-Non Finnish (NFE) AF: 0.607 AC: 31988 AN: 52678

Other (OTH) AF: 0.738 AC: 1104 AN: 1495

Alfa AF: 0.681 Hom.: 31275

Bravo AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs210465; hg19: chrX-82445926;