chrX-145988145-G-A

Position:

• chrX-145988145-G-A

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 0.32 in 111,339 control chromosomes in the GnomAD database, including 4,100 homozygotes. There are 10,450 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 0.32 (4100 hom., 10450 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595

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 (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.320 AC: 35586 AN: 111289 Hom.: 4087 Cov.: 23 AF XY: 0.311 AC XY: 10436 AN XY: 33521

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.320 AC: 35612 AN: 111339 Hom.: 4100 Cov.: 23 AF XY: 0.311 AC XY: 10450 AN XY: 33581

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.325

Alfa AF: 0.324 Hom.: 22738

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
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: rs1339597; hg19: chrX-145069663;