rs5929069

Positions:

• chrX-30153744-C-T

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 0.0126 in 111,435 control chromosomes in the GnomAD database, including 11 homozygotes. There are 395 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 0.013 (11 hom., 395 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

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 = 0.0126 (1400/111435) while in subpopulation NFE AF= 0.0186 (987/53065). AF 95% confidence interval is 0.0176. There are 11 homozygotes in gnomad4. There are 395 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30153744C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1400 AN: 111384 Hom.: 11 Cov.: 23 AF XY: 0.0118 AC XY: 395 AN XY: 33576

Gnomad AFR AF: 0.00255

Gnomad AMI AF: 0.0207

Gnomad AMR AF: 0.00592

Gnomad ASJ AF: 0.0151

Gnomad EAS AF: 0.000280

Gnomad SAS AF: 0.00271

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0140

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

GnomAD4 genome AF: 0.0126 AC: 1400 AN: 111435 Hom.: 11 Cov.: 23 AF XY: 0.0117 AC XY: 395 AN XY: 33637

Gnomad4 AFR AF: 0.00254

Gnomad4 AMR AF: 0.00591

Gnomad4 ASJ AF: 0.0151

Gnomad4 EAS AF: 0.000281

Gnomad4 SAS AF: 0.00272

Gnomad4 FIN AF: 0.0316

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0139

Alfa AF: 0.0173 Hom.: 265

Bravo AF: 0.0106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5929069; hg19: chrX-30171861;