19-55038944-A-G

Position:

• chr19-55038944-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593060.5(GP6-AS1):​n.156-3856A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,064 control chromosomes in the GnomAD database, including 50,699 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 0.81 (50699 hom., cov: 31)
• Consequence: GP6-AS1 ENST00000593060.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GP6-AS1	XR_001754012.3	n.122-3856A>G		intron_variant, non_coding_transcript_variant
GP6-AS1	XR_001754013.3	n.112-3856A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GP6-AS1	ENST00000593060.5	n.156-3856A>G		intron_variant, non_coding_transcript_variant		5
GP6-AS1	ENST00000586845.1	n.134-3888A>G		intron_variant, non_coding_transcript_variant		3
GP6-AS1	ENST00000586961.1	n.45-3888A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123612 AN: 151946 Hom.: 50673 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.813 AC: 123695 AN: 152064 Hom.: 50699 Cov.: 31 AF XY: 0.819 AC XY: 60852 AN XY: 74336

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.825

Alfa AF: 0.792 Hom.: 5973

Bravo AF: 0.805

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1654433; hg19: chr19-55550312;