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
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592311.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267320	ENST00000587140.5	TSL:5	n.277-8135A>T		intron	N/A
	ENSG00000267320	ENST00000592311.5	TSL:4	n.251-25621A>T		intron	N/A

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

African (AFR) AF: 0.131 AC: 5447 AN: 41500

American (AMR) AF: 0.137 AC: 2097 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5162

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4824

European-Finnish (FIN) AF: 0.00989 AC: 105 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00354 AC: 241 AN: 68020

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.65
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1006559; hg19: chr19-28836786;