chrX-146265017-A-G

Variant names:

• chrX-146265017-A-G
• rs4827700

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

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 0.64 (16968 hom., 20119 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).

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: 0.642 AC: 70469 AN: 109835 Hom.: 16978 Cov.: 22

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.612

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: 0.641 AC: 70486 AN: 109888 Hom.: 16968 Cov.: 22 AF XY: 0.626 AC XY: 20119 AN XY: 32136

African (AFR) AF: 0.826 AC: 24916 AN: 30173

American (AMR) AF: 0.472 AC: 4861 AN: 10294

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1504 AN: 2619

East Asian (EAS) AF: 0.692 AC: 2362 AN: 3415

South Asian (SAS) AF: 0.579 AC: 1475 AN: 2546

European-Finnish (FIN) AF: 0.531 AC: 3044 AN: 5732

Middle Eastern (MID) AF: 0.561 AC: 119 AN: 212

European-Non Finnish (NFE) AF: 0.588 AC: 30979 AN: 52712

Other (OTH) AF: 0.608 AC: 917 AN: 1509

Alfa AF: 0.587 Hom.: 48093

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4827700; hg19: chrX-145346535;