19-55013445-C-T

Position:

• chr19-55013445-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

GP6-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GP6-AS1	XR_001754012.3	n.121+6981C>T		intron_variant
GP6-AS1	XR_001754013.3	n.111+6981C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GP6-AS1	ENST00000586845.1	n.133+6981C>T		intron_variant		3
GP6-AS1	ENST00000593060.5	n.155+6981C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.474

Alfa AF: 0.495 Hom.: 33708

Bravo AF: 0.440

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1654410; hg19: chr19-55524813;