rs1582598

Variant names:

• chr16-59289318-A-G
• rs1582598
• ENST00000775136.1:n.-138A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000775136.1(ENSG00000300932):​n.-138A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,098 control chromosomes in the GnomAD database, including 4,542 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 0.17 (4542 hom., cov: 32)
• Consequence: ENSG00000300932 ENST00000775136.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 2 publications found

Genes affected

ENSG00000300932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 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
ENSG00000300932	ENST00000775136.1	n.-138A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25693 AN: 151980 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.169 AC: 25731 AN: 152098 Hom.: 4542 Cov.: 32 AF XY: 0.172 AC XY: 12778 AN XY: 74358

African (AFR) AF: 0.429 AC: 17789 AN: 41422

American (AMR) AF: 0.104 AC: 1594 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2119 AN: 5156

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4822

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10608

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0290 AC: 1975 AN: 68016

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.125 Hom.: 646

Bravo AF: 0.186

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	19
DANN	Benign	0.71
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1582598; hg19: chr16-59323222;