X-67140772-T-C

Variant names:

• chrX-67140772-T-C
• rs5919287

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 0.66 (20423 hom., 21605 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• 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=-0.94).

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: 0.657 AC: 72283 AN: 109971 Hom.: 20430 Cov.: 22

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.702

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: 0.657 AC: 72278 AN: 110025 Hom.: 20423 Cov.: 22 AF XY: 0.667 AC XY: 21605 AN XY: 32415

African (AFR) AF: 0.155 AC: 4733 AN: 30487

American (AMR) AF: 0.829 AC: 8460 AN: 10201

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 2413 AN: 2622

East Asian (EAS) AF: 0.999 AC: 3424 AN: 3429

South Asian (SAS) AF: 0.917 AC: 2325 AN: 2536

European-Finnish (FIN) AF: 0.828 AC: 4786 AN: 5777

Middle Eastern (MID) AF: 0.759 AC: 164 AN: 216

European-Non Finnish (NFE) AF: 0.843 AC: 44322 AN: 52587

Other (OTH) AF: 0.704 AC: 1049 AN: 1491

Alfa AF: 0.758 Hom.: 29907

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs5919287; hg19: chrX-66360614;