chrX-19168560-C-G

Variant names:

• chrX-19168560-C-G
• rs5955711

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.326 AC: 36272 AN: 111186 Hom.: 8554 Cov.: 23

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

African (AFR) AF: 0.846 AC: 25727 AN: 30420

American (AMR) AF: 0.153 AC: 1607 AN: 10494

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 364 AN: 2632

East Asian (EAS) AF: 0.0635 AC: 226 AN: 3559

South Asian (SAS) AF: 0.280 AC: 737 AN: 2630

European-Finnish (FIN) AF: 0.110 AC: 662 AN: 6030

Middle Eastern (MID) AF: 0.240 AC: 52 AN: 217

European-Non Finnish (NFE) AF: 0.121 AC: 6410 AN: 53058

Other (OTH) AF: 0.286 AC: 435 AN: 1523

Alfa AF: 0.245 Hom.: 1772

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.69
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs5955711; hg19: chrX-19186678;