X-33606299-T-A

Variant names:

• chrX-33606299-T-A
• rs1356619

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 0.86 (28877 hom., 28066 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• 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=-1.02).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.859 AC: 94665 AN: 110181 Hom.: 28878 Cov.: 22

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.903

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.862

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: 0.859 AC: 94715 AN: 110230 Hom.: 28877 Cov.: 22 AF XY: 0.864 AC XY: 28066 AN XY: 32472

African (AFR) AF: 0.971 AC: 29412 AN: 30299

American (AMR) AF: 0.875 AC: 9071 AN: 10365

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2048 AN: 2632

East Asian (EAS) AF: 1.00 AC: 3463 AN: 3464

South Asian (SAS) AF: 0.963 AC: 2454 AN: 2549

European-Finnish (FIN) AF: 0.855 AC: 4976 AN: 5819

Middle Eastern (MID) AF: 0.899 AC: 195 AN: 217

European-Non Finnish (NFE) AF: 0.782 AC: 41218 AN: 52706

Other (OTH) AF: 0.864 AC: 1297 AN: 1501

Alfa AF: 0.827 Hom.: 7096

Bravo AF: 0.867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1356619; hg19: chrX-33624416; COSMIC: COSV58358359;