X-123016678-G-T

Variant names:

• chrX-123016678-G-T
• rs1151742

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 0.83 (26711 hom., 26596 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• 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=-0.9).

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: 0.826 AC: 90781 AN: 109957 Hom.: 26714 Cov.: 22

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.907

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.841

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: 0.826 AC: 90822 AN: 110009 Hom.: 26711 Cov.: 22 AF XY: 0.824 AC XY: 26596 AN XY: 32289

African (AFR) AF: 0.760 AC: 22994 AN: 30246

American (AMR) AF: 0.770 AC: 7928 AN: 10294

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 2490 AN: 2637

East Asian (EAS) AF: 0.631 AC: 2195 AN: 3480

South Asian (SAS) AF: 0.832 AC: 2160 AN: 2596

European-Finnish (FIN) AF: 0.831 AC: 4731 AN: 5691

Middle Eastern (MID) AF: 0.916 AC: 197 AN: 215

European-Non Finnish (NFE) AF: 0.878 AC: 46264 AN: 52684

Other (OTH) AF: 0.840 AC: 1251 AN: 1490

Alfa AF: 0.782 Hom.: 5042

Bravo AF: 0.815

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.62
PhyloP100		0.66

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: rs1151742; hg19: chrX-122150531;