rs1590919

Positions:

• chr13-104362873-G-A

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 0.219 in 151,964 control chromosomes in the GnomAD database, including 3,927 homozygotes. 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 0.22 (3927 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104362873G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33183 AN: 151846 Hom.: 3920 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.219 AC: 33221 AN: 151964 Hom.: 3927 Cov.: 31 AF XY: 0.223 AC XY: 16545 AN XY: 74292

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.196

Alfa AF: 0.194 Hom.: 6104

Bravo AF: 0.218

Asia WGS AF: 0.318 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1590919; hg19: chr13-105015223;