X-19240194-A-G

Position:

• chrX-19240194-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 0.288 in 110,857 control chromosomes in the GnomAD database, including 7,652 homozygotes. There are 8,985 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 0.29 (7652 hom., 8985 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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: 0.287 AC: 31850 AN: 110805 Hom.: 7645 Cov.: 21 AF XY: 0.270 AC XY: 8938 AN XY: 33067

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.0555

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.288 AC: 31909 AN: 110857 Hom.: 7652 Cov.: 21 AF XY: 0.271 AC XY: 8985 AN XY: 33129

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.0871

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.0466

Gnomad4 OTH AF: 0.256

Alfa AF: 0.209 Hom.: 1828

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10218356; hg19: chrX-19258312;