X-146305041-G-T

Position:

• chrX-146305041-G-T

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 0.414 in 110,982 control chromosomes in the GnomAD database, including 6,976 homozygotes. There are 13,987 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 0.41 (6976 hom., 13987 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 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: 0.414 AC: 45953 AN: 110927 Hom.: 6972 Cov.: 23 AF XY: 0.420 AC XY: 13951 AN XY: 33205

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.414 AC: 45994 AN: 110982 Hom.: 6976 Cov.: 23 AF XY: 0.420 AC XY: 13987 AN XY: 33270

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.437

Alfa AF: 0.435 Hom.: 10355

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5920070; hg19: chrX-145386559;