rs5945642

Variant names:

• chrX-51557826-G-A
• rs5945642

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0165 in 112,549 control chromosomes in the GnomAD database, including 28 homozygotes. There are 612 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 0.017 (28 hom., 612 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0165 (1860/112549) while in subpopulation NFE AF = 0.0233 (1243/53326). AF 95% confidence interval is 0.0222. There are 28 homozygotes in GnomAd4. There are 612 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 gene

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: 0.0165 AC: 1859 AN: 112496 Hom.: 28 Cov.: 23

Gnomad AFR AF: 0.00265

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.00942

Gnomad ASJ AF: 0.00752

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.00837

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0178

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

GnomAD4 genome AF: 0.0165 AC: 1860 AN: 112549 Hom.: 28 Cov.: 23 AF XY: 0.0176 AC XY: 612 AN XY: 34717

African (AFR) AF: 0.00264 AC: 82 AN: 31029

American (AMR) AF: 0.00941 AC: 100 AN: 10624

Ashkenazi Jewish (ASJ) AF: 0.00752 AC: 20 AN: 2659

East Asian (EAS) AF: 0.00 AC: 0 AN: 3594

South Asian (SAS) AF: 0.00474 AC: 13 AN: 2743

European-Finnish (FIN) AF: 0.0368 AC: 226 AN: 6146

Middle Eastern (MID) AF: 0.00917 AC: 2 AN: 218

European-Non Finnish (NFE) AF: 0.0233 AC: 1243 AN: 53326

Other (OTH) AF: 0.0176 AC: 27 AN: 1532

Alfa AF: 0.0198 Hom.: 468

Bravo AF: 0.0147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.15
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs5945642; hg19: chrX-51300678;