X-100510088-G-C

Variant names:

• chrX-100510088-G-C
• rs768198

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 0.63 (17441 hom., 19621 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• 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=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.631 AC: 69440 AN: 110052 Hom.: 17439 Cov.: 22

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.604

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: 0.631 AC: 69494 AN: 110103 Hom.: 17441 Cov.: 22 AF XY: 0.607 AC XY: 19621 AN XY: 32345

African (AFR) AF: 0.930 AC: 28222 AN: 30344

American (AMR) AF: 0.509 AC: 5234 AN: 10292

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1457 AN: 2627

East Asian (EAS) AF: 0.279 AC: 979 AN: 3505

South Asian (SAS) AF: 0.273 AC: 712 AN: 2605

European-Finnish (FIN) AF: 0.432 AC: 2478 AN: 5742

Middle Eastern (MID) AF: 0.663 AC: 138 AN: 208

European-Non Finnish (NFE) AF: 0.551 AC: 29001 AN: 52608

Other (OTH) AF: 0.602 AC: 909 AN: 1509

Alfa AF: 0.354 Hom.: 1381

Bravo AF: 0.650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.57
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs768198; hg19: chrX-99765085;