19-28334588-A-G

Variant names:

• chr19-28334588-A-G
• rs8111948
• ENST00000587140.5:n.530-1759T>C

Variant summary

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

The ENST00000587140.5(ENSG00000267320):​n.530-1759T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,016 control chromosomes in the GnomAD database, including 13,782 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 0.39 (13782 hom., cov: 32)
• Consequence: ENSG00000267320 ENST00000587140.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 2 publications found

Genes affected

ENSG00000267320 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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
ENSG00000267320	ENST00000587140.5	n.530-1759T>C		intron_variant	Intron 4 of 4	5
ENSG00000267320	ENST00000592311.5	n.251-14330T>C		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59233 AN: 151898 Hom.: 13781 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.390 AC: 59240 AN: 152016 Hom.: 13782 Cov.: 32 AF XY: 0.398 AC XY: 29567 AN XY: 74316

African (AFR) AF: 0.138 AC: 5713 AN: 41450

American (AMR) AF: 0.422 AC: 6446 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1625 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5160

South Asian (SAS) AF: 0.584 AC: 2817 AN: 4822

European-Finnish (FIN) AF: 0.582 AC: 6155 AN: 10570

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33573 AN: 67944

Other (OTH) AF: 0.402 AC: 849 AN: 2112

Alfa AF: 0.419 Hom.: 6325

Bravo AF: 0.361

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs8111948; hg19: chr19-28825495;