X-151981661-G-T

Variant names:

• chrX-151981661-G-T
• rs1981452

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 0.57 (13027 hom., 17774 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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: 0.574 AC: 62443 AN: 108870 Hom.: 13030 Cov.: 21

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.648

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.582

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: 0.574 AC: 62482 AN: 108925 Hom.: 13027 Cov.: 21 AF XY: 0.568 AC XY: 17774 AN XY: 31295

African (AFR) AF: 0.617 AC: 18397 AN: 29819

American (AMR) AF: 0.626 AC: 6433 AN: 10277

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1341 AN: 2622

East Asian (EAS) AF: 0.704 AC: 2387 AN: 3391

South Asian (SAS) AF: 0.713 AC: 1732 AN: 2430

European-Finnish (FIN) AF: 0.493 AC: 2793 AN: 5663

Middle Eastern (MID) AF: 0.646 AC: 135 AN: 209

European-Non Finnish (NFE) AF: 0.535 AC: 28038 AN: 52366

Other (OTH) AF: 0.583 AC: 864 AN: 1482

Alfa AF: 0.558 Hom.: 12658

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.74
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1981452; hg19: chrX-151150133;