rs527480

Positions:

• chrX-74416032-C-T

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 0.373 in 110,453 control chromosomes in the GnomAD database, including 6,166 homozygotes. There are 12,224 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 0.37 (6166 hom., 12224 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74416032C>T		intergenic_region
LOC105373252	XR_007068267.1	n.344-471G>A		intron_variant
LOC105373252	XR_938445.3	n.344-471G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.373 AC: 41145 AN: 110400 Hom.: 6166 Cov.: 23 AF XY: 0.373 AC XY: 12183 AN XY: 32654

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.373 AC: 41189 AN: 110453 Hom.: 6166 Cov.: 23 AF XY: 0.374 AC XY: 12224 AN XY: 32719

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.297

Alfa AF: 0.324 Hom.: 8148

Bravo AF: 0.370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs527480; hg19: chrX-73635867;