rs1006559

Variant names:

• chr19-28345879-T-A
• rs1006559
• ENST00000587140.5:n.277-8135A>T

Variant summary

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

The ENST00000592311.5(ENSG00000267320):​n.251-25621A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,202 control chromosomes in the GnomAD database, including 695 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 0.062 (695 hom., cov: 32)
• Consequence: ENSG00000267320 ENST00000592311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

Genes affected

ENSG00000267320 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 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.277-8135A>T		intron_variant	Intron 3 of 4	5
ENSG00000267320	ENST00000592311.5	n.251-25621A>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.0619 AC: 9412 AN: 152084 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00354

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0621 AC: 9449 AN: 152202 Hom.: 695 Cov.: 32 AF XY: 0.0637 AC XY: 4740 AN XY: 74426

Gnomad4 AFR AF: 0.131 AC: 0.131253 AN: 0.131253

Gnomad4 AMR AF: 0.137 AC: 0.137131 AN: 0.137131

Gnomad4 ASJ AF: 0.00807 AC: 0.00807382 AN: 0.00807382

Gnomad4 EAS AF: 0.245 AC: 0.24506 AN: 0.24506

Gnomad4 SAS AF: 0.0299 AC: 0.0298507 AN: 0.0298507

Gnomad4 FIN AF: 0.00989 AC: 0.00989073 AN: 0.00989073

Gnomad4 NFE AF: 0.00354 AC: 0.00354308 AN: 0.00354308

Gnomad4 OTH AF: 0.0539 AC: 0.0539262 AN: 0.0539262

Alfa AF: 0.0356 Hom.: 43

Bravo AF: 0.0773

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1006559; hg19: chr19-28836786;