X-28213017-A-G

Variant names:

• chrX-28213017-A-G
• rs5926352

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 0.58 (13486 hom., 18863 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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: 0.582 AC: 63932 AN: 109905 Hom.: 13486 Cov.: 22

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.555

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.575

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: 0.582 AC: 63959 AN: 109956 Hom.: 13486 Cov.: 22 AF XY: 0.585 AC XY: 18863 AN XY: 32248

African (AFR) AF: 0.438 AC: 13283 AN: 30295

American (AMR) AF: 0.655 AC: 6763 AN: 10318

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1497 AN: 2628

East Asian (EAS) AF: 0.835 AC: 2854 AN: 3416

South Asian (SAS) AF: 0.556 AC: 1419 AN: 2554

European-Finnish (FIN) AF: 0.673 AC: 3836 AN: 5699

Middle Eastern (MID) AF: 0.540 AC: 116 AN: 215

European-Non Finnish (NFE) AF: 0.624 AC: 32833 AN: 52652

Other (OTH) AF: 0.579 AC: 870 AN: 1502

Alfa AF: 0.596 Hom.: 45943

Bravo AF: 0.583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.81
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs5926352; hg19: chrX-28231134;