ENST00000589999.1:n.110-28991A>G

Variant names:

• chr19-28522014-T-C
• rs8113142
• ENST00000589999.1:n.110-28991A>G

Variant summary

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

The ENST00000589999.1(ENSG00000290606):​n.110-28991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,242 control chromosomes in the GnomAD database, including 4,590 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 0.23 (4590 hom., cov: 31)
• Consequence: ENSG00000290606 ENST00000589999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 4 publications found

Genes affected

ENSG00000290606 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589999.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100420587	NR_110759.1		n.657-55234A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290606	ENST00000589999.1	TSL:1	n.110-28991A>G		intron	N/A
	ENSG00000290606	ENST00000592347.5	TSL:1	n.643-55234A>G		intron	N/A
	ENSG00000290606	ENST00000593065.6	TSL:3	n.178+13086A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34148 AN: 151122 Hom.: 4583 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.226 AC: 34181 AN: 151242 Hom.: 4590 Cov.: 31 AF XY: 0.226 AC XY: 16649 AN XY: 73810

African (AFR) AF: 0.371 AC: 15272 AN: 41212

American (AMR) AF: 0.184 AC: 2778 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1328 AN: 5128

South Asian (SAS) AF: 0.144 AC: 683 AN: 4736

European-Finnish (FIN) AF: 0.192 AC: 2002 AN: 10420

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10428 AN: 67880

Other (OTH) AF: 0.221 AC: 461 AN: 2084

Alfa AF: 0.180 Hom.: 9136

Bravo AF: 0.233

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs8113142; hg19: chr19-29012921;