19-55013445-C-T

Variant names:

• chr19-55013445-C-T
• rs1654410
• ENST00000586845.1:n.133+6981C>T

Variant summary

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

The ENST00000586845.1(GP6-AS1):​n.133+6981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,838 control chromosomes in the GnomAD database, including 16,685 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 0.46 (16685 hom., cov: 31)
• Consequence: GP6-AS1 ENST00000586845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 18 publications found

Genes affected

GP6-AS1 (HGNC:55305): (GP6 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586845.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GP6-AS1	ENST00000586845.1	TSL:3	n.133+6981C>T		intron	N/A
	GP6-AS1	ENST00000593060.5	TSL:5	n.155+6981C>T		intron	N/A
	GP6-AS1	ENST00000778584.1		n.156+6981C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69722 AN: 151718 Hom.: 16686 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.459 AC: 69751 AN: 151838 Hom.: 16685 Cov.: 31 AF XY: 0.462 AC XY: 34284 AN XY: 74210

African (AFR) AF: 0.333 AC: 13779 AN: 41354

American (AMR) AF: 0.436 AC: 6645 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3192 AN: 5156

South Asian (SAS) AF: 0.379 AC: 1828 AN: 4824

European-Finnish (FIN) AF: 0.592 AC: 6248 AN: 10550

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 35130 AN: 67942

Other (OTH) AF: 0.474 AC: 1000 AN: 2110

Alfa AF: 0.491 Hom.: 76964

Bravo AF: 0.440

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1654410; hg19: chr19-55524813;