19-34357346-G-T

Variant names:

• chr19-34357346-G-T
• rs580391
• ENST00000591311.2:n.520+1139C>A

Variant summary

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

The ENST00000591311.2(ENSG00000267219):​n.520+1139C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,094 control chromosomes in the GnomAD database, including 5,078 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 0.24 (5078 hom., cov: 32)
• Consequence: ENSG00000267219 ENST00000591311.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 3 publications found

Genes affected

ENSG00000267219 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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
ENSG00000267219	ENST00000591311.2	n.520+1139C>A		intron_variant	Intron 2 of 2	3
ENSG00000267219	ENST00000849863.1	n.524+1139C>A		intron_variant	Intron 2 of 2
ENSG00000267219	ENST00000849864.1	n.797+1139C>A		intron_variant	Intron 1 of 1
ENSG00000267219	ENST00000849865.1	n.510+1139C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37164 AN: 151976 Hom.: 5071 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.245 AC: 37191 AN: 152094 Hom.: 5078 Cov.: 32 AF XY: 0.246 AC XY: 18274 AN XY: 74358

African (AFR) AF: 0.244 AC: 10110 AN: 41492

American (AMR) AF: 0.199 AC: 3045 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.618 AC: 3195 AN: 5166

South Asian (SAS) AF: 0.214 AC: 1036 AN: 4830

European-Finnish (FIN) AF: 0.251 AC: 2653 AN: 10560

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15615 AN: 67968

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.149 Hom.: 369

Bravo AF: 0.242

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.38
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs580391; hg19: chr19-34848251;