rs1551512

Positions:

• chr8-127111881-T-G

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 0.165 in 152,110 control chromosomes in the GnomAD database, including 4,810 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 0.16 (4810 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127111881T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000642100.1	n.418-32748A>C		intron_variant
PCAT1	ENST00000645463.1	n.855+105263T>G		intron_variant
PCAT1	ENST00000646670.1	n.1064+98107T>G		intron_variant
PCAT1	ENST00000647190.2	n.1191+62581T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25004 AN: 151992 Hom.: 4792 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.165 AC: 25074 AN: 152110 Hom.: 4810 Cov.: 32 AF XY: 0.162 AC XY: 12047 AN XY: 74386

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0506

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0862 Hom.: 869

Bravo AF: 0.179

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551512; hg19: chr8-128124126;