rs5945642

Positions:

• chrX-51557826-G-A

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.51557826G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0165 AC: 1859 AN: 112496 Hom.: 28 Cov.: 23 AF XY: 0.0176 AC XY: 611 AN XY: 34654

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

Gnomad4 AFR AF: 0.00264

Gnomad4 AMR AF: 0.00941

Gnomad4 ASJ AF: 0.00752

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00474

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0176

Alfa AF: 0.0215 Hom.: 325

Bravo AF: 0.0147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945642; hg19: chrX-51300678;