rs5991573

Positions:

• chrX-43070861-T-C

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 0.159 in 111,420 control chromosomes in the GnomAD database, including 2,819 homozygotes. There are 4,930 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 0.16 (2819 hom., 4930 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43070861T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 17684 AN: 111368 Hom.: 2816 Cov.: 23 AF XY: 0.146 AC XY: 4908 AN XY: 33630

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0856

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0251

Gnomad NFE AF: 0.00765

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.159 AC: 17722 AN: 111420 Hom.: 2819 Cov.: 23 AF XY: 0.146 AC XY: 4930 AN XY: 33692

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.0853

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.00765

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0810 Hom.: 1130

Bravo AF: 0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5991573; hg19: chrX-42930110;