chrX-50901769-A-G

Position:

• chrX-50901769-A-G

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 0.218 in 110,975 control chromosomes in the GnomAD database, including 2,828 homozygotes. There are 6,794 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 0.22 (2828 hom., 6794 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.218 AC: 24127 AN: 110922 Hom.: 2819 Cov.: 22 AF XY: 0.204 AC XY: 6765 AN XY: 33154

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.218 AC: 24171 AN: 110975 Hom.: 2828 Cov.: 22 AF XY: 0.205 AC XY: 6794 AN XY: 33217

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.206

Alfa AF: 0.192 Hom.: 1870

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6521896; hg19: chrX-50644769;