X-136072759-A-G

Variant names:

• chrX-136072759-A-G
• rs1994878

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 0.98 (37148 hom., 32119 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• 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=-1.02).

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: 0.977 AC: 108077 AN: 110644 Hom.: 37153 Cov.: 23

Gnomad AFR AF: 0.929

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.989

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.992

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.987

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: 0.977 AC: 108129 AN: 110698 Hom.: 37148 Cov.: 23 AF XY: 0.978 AC XY: 32119 AN XY: 32858

African (AFR) AF: 0.929 AC: 28297 AN: 30463

American (AMR) AF: 0.989 AC: 10180 AN: 10297

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2630 AN: 2631

East Asian (EAS) AF: 1.00 AC: 3522 AN: 3522

South Asian (SAS) AF: 0.999 AC: 2543 AN: 2545

European-Finnish (FIN) AF: 0.997 AC: 5808 AN: 5827

Middle Eastern (MID) AF: 0.991 AC: 213 AN: 215

European-Non Finnish (NFE) AF: 0.995 AC: 52770 AN: 53012

Other (OTH) AF: 0.987 AC: 1486 AN: 1506

Alfa AF: 0.977 Hom.: 3308

Bravo AF: 0.974

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.21
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1994878; hg19: chrX-135154918;