rs7001069

Positions:

• chr8-127098401-A-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 0.127 in 152,092 control chromosomes in the GnomAD database, including 2,596 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 0.13 (2596 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127098401A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000642100.1	n.418-19268T>C		intron_variant
PCAT1	ENST00000645463.1	n.855+91783A>G		intron_variant
PCAT1	ENST00000646670.1	n.1064+84627A>G		intron_variant
PCAT1	ENST00000647190.2	n.1191+49101A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19195 AN: 151974 Hom.: 2585 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.127 AC: 19245 AN: 152092 Hom.: 2596 Cov.: 32 AF XY: 0.125 AC XY: 9312 AN XY: 74344

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0510

Gnomad4 NFE AF: 0.0319

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0705 Hom.: 353

Bravo AF: 0.135

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7001069; hg19: chr8-128110646;