rs1456305

Positions:

• chr8-127115007-G-A
• chr8-127115007-G-T

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 0.879 in 152,176 control chromosomes in the GnomAD database, including 58,892 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 0.88 (58892 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127115007G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000642100.1	n.418-35874C>T		intron_variant
PCAT1	ENST00000645463.1	n.855+108389G>A		intron_variant
PCAT1	ENST00000646670.1	n.1064+101233G>A		intron_variant
PCAT1	ENST00000647190.2	n.1191+65707G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133635 AN: 152058 Hom.: 58859 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.879 AC: 133724 AN: 152176 Hom.: 58892 Cov.: 31 AF XY: 0.874 AC XY: 64997 AN XY: 74366

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.876

Alfa AF: 0.873 Hom.: 78188

Bravo AF: 0.878

Asia WGS AF: 0.899 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.098
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456305; hg19: chr8-128127252;