rs1590919

Variant names:

• chr13-104362873-G-A
• rs1590919
• ENST00000844365.1:n.103-3504G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000844365.1(ENSG00000309849):​n.103-3504G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309849 ENST00000844365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 5 publications found

Genes affected

ENSG00000309849 (HGNC:):

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309849	ENST00000844365.1	n.103-3504G>A		intron_variant	Intron 1 of 2
ENSG00000309849	ENST00000844366.1	n.104+5124G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.221 AC: 9154 AN: 41448

American (AMR) AF: 0.238 AC: 3627 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2112 AN: 5130

South Asian (SAS) AF: 0.191 AC: 919 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2878 AN: 10560

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13668 AN: 67960

Other (OTH) AF: 0.196 AC: 413 AN: 2112

Alfa AF: 0.200 Hom.: 10097

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1590919; hg19: chr13-105015223;