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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs1151742; hg19: chrX-122150531;