X-45773413-G-A

Position:

• chrX-45773413-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 110,545 control chromosomes in the GnomAD database, including 5,617 homozygotes. There are 10,144 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 (5617 hom., 10144 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 35312 AN: 110492 Hom.: 5609 Cov.: 22 AF XY: 0.308 AC XY: 10103 AN XY: 32798

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.0365

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.320 AC: 35363 AN: 110545 Hom.: 5617 Cov.: 22 AF XY: 0.309 AC XY: 10144 AN XY: 32861

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.325

Alfa AF: 0.216 Hom.: 4846

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6521038; hg19: chrX-45632816;