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).

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: 0.977 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 v4.3

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;