X-152487090-T-C

Variant names:

• chrX-152487090-T-C
• rs10856240

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 (16982 hom., 20349 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• 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=-0.96).

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: 0.626 AC: 69066 AN: 110244 Hom.: 16993 Cov.: 23

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.638

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: 0.626 AC: 69056 AN: 110293 Hom.: 16982 Cov.: 23 AF XY: 0.625 AC XY: 20349 AN XY: 32579

African (AFR) AF: 0.328 AC: 10003 AN: 30453

American (AMR) AF: 0.565 AC: 5838 AN: 10341

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1783 AN: 2635

East Asian (EAS) AF: 0.416 AC: 1439 AN: 3455

South Asian (SAS) AF: 0.616 AC: 1622 AN: 2631

European-Finnish (FIN) AF: 0.851 AC: 4870 AN: 5721

Middle Eastern (MID) AF: 0.726 AC: 151 AN: 208

European-Non Finnish (NFE) AF: 0.793 AC: 41760 AN: 52674

Other (OTH) AF: 0.629 AC: 940 AN: 1495

Alfa AF: 0.649 Hom.: 29159

Bravo AF: 0.594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10856240; hg19: chrX-151655562;