X-84249323-C-T

Variant names:

• chrX-84249323-C-T
• rs765076

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 0.55 (12040 hom., 16450 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

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: 0.555 AC: 59450 AN: 107208 Hom.: 12048 Cov.: 20

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.558

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: 0.555 AC: 59480 AN: 107250 Hom.: 12040 Cov.: 20 AF XY: 0.552 AC XY: 16450 AN XY: 29774

African (AFR) AF: 0.557 AC: 16412 AN: 29472

American (AMR) AF: 0.654 AC: 6517 AN: 9962

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1381 AN: 2593

East Asian (EAS) AF: 0.760 AC: 2565 AN: 3376

South Asian (SAS) AF: 0.571 AC: 1350 AN: 2366

European-Finnish (FIN) AF: 0.432 AC: 2232 AN: 5165

Middle Eastern (MID) AF: 0.544 AC: 111 AN: 204

European-Non Finnish (NFE) AF: 0.532 AC: 27686 AN: 51993

Other (OTH) AF: 0.555 AC: 806 AN: 1451

Alfa AF: 0.541 Hom.: 70998

Bravo AF: 0.570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs765076; hg19: chrX-83504331;