rs6993569

Positions:

• chr8-127071852-G-A

Variant summary

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

The variant allele was found at a frequency of 0.187 in 152,046 control chromosomes in the GnomAD database, including 4,839 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 0.19 (4839 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127071852G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000645463.1	n.855+65234G>A		intron_variant
PCAT1	ENST00000646670.1	n.1064+58078G>A		intron_variant
PCAT1	ENST00000647190.2	n.1191+22552G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28382 AN: 151930 Hom.: 4823 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.187 AC: 28449 AN: 152046 Hom.: 4839 Cov.: 32 AF XY: 0.188 AC XY: 13994 AN XY: 74348

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0806 Hom.: 1877

Bravo AF: 0.205

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6993569; hg19: chr8-128084097;