chrX-146004438-C-A

Variant names:

• chrX-146004438-C-A
• rs2202091

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 0.60 (14349 hom., 17793 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• 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=-1.01).

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: 0.599 AC: 64367 AN: 107420 Hom.: 14338 Cov.: 21

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.572

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: 0.599 AC: 64413 AN: 107463 Hom.: 14349 Cov.: 21 AF XY: 0.593 AC XY: 17793 AN XY: 29991

African (AFR) AF: 0.737 AC: 21769 AN: 29544

American (AMR) AF: 0.554 AC: 5483 AN: 9903

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1137 AN: 2603

East Asian (EAS) AF: 0.590 AC: 1985 AN: 3362

South Asian (SAS) AF: 0.637 AC: 1537 AN: 2413

European-Finnish (FIN) AF: 0.551 AC: 2893 AN: 5246

Middle Eastern (MID) AF: 0.588 AC: 124 AN: 211

European-Non Finnish (NFE) AF: 0.545 AC: 28372 AN: 52064

Other (OTH) AF: 0.575 AC: 839 AN: 1460

Alfa AF: 0.577 Hom.: 4341

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2202091; hg19: chrX-145085956;