chrX-19168560-C-G

Variant names:

• chrX-19168560-C-G
• rs5955711

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 0.327 in 111,238 control chromosomes in the GnomAD database, including 8,561 homozygotes. There are 10,283 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 0.33 (8561 hom., 10283 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.326 AC: 36272 AN: 111186 Hom.: 8554 Cov.: 23 AF XY: 0.306 AC XY: 10232 AN XY: 33426

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.327 AC: 36333 AN: 111238 Hom.: 8561 Cov.: 23 AF XY: 0.307 AC XY: 10283 AN XY: 33488

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0635

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.286

Alfa AF: 0.245 Hom.: 1772

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5955711; hg19: chrX-19186678;