rs5991573

Variant names:

• chrX-43070861-T-C
• rs5991573

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.159 AC: 17684 AN: 111368 Hom.: 2816 Cov.: 23

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

African (AFR) AF: 0.488 AC: 14824 AN: 30402

American (AMR) AF: 0.0853 AC: 898 AN: 10533

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 55 AN: 2646

East Asian (EAS) AF: 0.240 AC: 845 AN: 3523

South Asian (SAS) AF: 0.115 AC: 304 AN: 2649

European-Finnish (FIN) AF: 0.0293 AC: 178 AN: 6071

Middle Eastern (MID) AF: 0.0275 AC: 6 AN: 218

European-Non Finnish (NFE) AF: 0.00765 AC: 407 AN: 53173

Other (OTH) AF: 0.135 AC: 205 AN: 1519

Alfa AF: 0.0847 Hom.: 1401

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs5991573; hg19: chrX-42930110;