rs2179965

Positions:

• chr1-88336329-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.172 in 152,062 control chromosomes in the GnomAD database, including 2,401 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 0.17 (2401 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.88336329A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKN2-AS1	ENST00000645056.1	n.470+192507T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26146 AN: 151944 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.172 AC: 26176 AN: 152062 Hom.: 2401 Cov.: 32 AF XY: 0.174 AC XY: 12905 AN XY: 74346

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.137

Alfa AF: 0.164 Hom.: 4737

Bravo AF: 0.172

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	18
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2179965; hg19: chr1-88802012;