X-146489384-A-G

Variant names:

• chrX-146489384-A-G
• rs2891837

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.29 (3976 hom., 7842 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.295 AC: 30260 AN: 102518 Hom.: 3981 Cov.: 20

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.295 AC: 30247 AN: 102540 Hom.: 3976 Cov.: 20 AF XY: 0.296 AC XY: 7842 AN XY: 26472

African (AFR) AF: 0.0943 AC: 2612 AN: 27707

American (AMR) AF: 0.381 AC: 3494 AN: 9175

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1029 AN: 2533

East Asian (EAS) AF: 0.158 AC: 509 AN: 3221

South Asian (SAS) AF: 0.329 AC: 716 AN: 2179

European-Finnish (FIN) AF: 0.346 AC: 1592 AN: 4601

Middle Eastern (MID) AF: 0.362 AC: 72 AN: 199

European-Non Finnish (NFE) AF: 0.383 AC: 19486 AN: 50929

Other (OTH) AF: 0.318 AC: 431 AN: 1355

Alfa AF: 0.334 Hom.: 11187

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.42
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2891837; hg19: chrX-145570902;