X-146489384-A-G

Variant names:

• chrX-146489384-A-G
• rs2891837

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.295 AC: 30260 AN: 102518 Hom.: 3981 Cov.: 20 AF XY: 0.297 AC XY: 7841 AN XY: 26434

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

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.318

Alfa AF: 0.349 Hom.: 7863

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2891837; hg19: chrX-145570902;