rs17249566

Positions:

• chrX-50901254-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 0.0513 in 111,563 control chromosomes in the GnomAD database, including 158 homozygotes. There are 1,617 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 0.051 (158 hom., 1617 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.071 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50901254C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 5713 AN: 111509 Hom.: 158 Cov.: 22 AF XY: 0.0479 AC XY: 1612 AN XY: 33681

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0145

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.0101

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0672

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0513 AC: 5718 AN: 111563 Hom.: 158 Cov.: 22 AF XY: 0.0479 AC XY: 1617 AN XY: 33745

Gnomad4 AFR AF: 0.0173

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.0930

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0753

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0729

Gnomad4 OTH AF: 0.0576

Alfa AF: 0.0677 Hom.: 437

Bravo AF: 0.0465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
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: rs17249566; hg19: chrX-50644254;