X-146282868-A-G

Variant names:

• chrX-146282868-A-G
• rs5966108

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.365 in 110,745 control chromosomes in the GnomAD database, including 5,471 homozygotes. There are 11,847 hemizygotes in GnomAD. 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 0.36 (5471 hom., 11847 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.494 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: 0.365 AC: 40354 AN: 110691 Hom.: 5464 Cov.: 23 AF XY: 0.358 AC XY: 11810 AN XY: 32969

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.365 AC: 40408 AN: 110745 Hom.: 5471 Cov.: 23 AF XY: 0.359 AC XY: 11847 AN XY: 33033

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.372

Alfa AF: 0.392 Hom.: 2923

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5966108; hg19: chrX-145364386;