rs5990890

Variant names:

• chrX-20575680-T-G
• rs5990890

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 0.23 in 110,958 control chromosomes in the GnomAD database, including 2,946 homozygotes. There are 7,458 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 0.23 (2946 hom., 7458 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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: 0.230 AC: 25486 AN: 110903 Hom.: 2942 Cov.: 22

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.230 AC: 25517 AN: 110958 Hom.: 2946 Cov.: 22 AF XY: 0.225 AC XY: 7458 AN XY: 33188

African (AFR) AF: 0.443 AC: 13480 AN: 30400

American (AMR) AF: 0.239 AC: 2501 AN: 10447

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 452 AN: 2646

East Asian (EAS) AF: 0.257 AC: 896 AN: 3480

South Asian (SAS) AF: 0.153 AC: 402 AN: 2625

European-Finnish (FIN) AF: 0.215 AC: 1279 AN: 5955

Middle Eastern (MID) AF: 0.242 AC: 52 AN: 215

European-Non Finnish (NFE) AF: 0.115 AC: 6069 AN: 52985

Other (OTH) AF: 0.234 AC: 356 AN: 1523

Alfa AF: 0.191 Hom.: 1251

Bravo AF: 0.246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.68
DANN	Benign	0.53
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs5990890; hg19: chrX-20593798;