rs1789964

Positions:

• chr8-108514499-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 0.127 in 152,184 control chromosomes in the GnomAD database, including 1,676 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 (1676 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.108514499G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19351 AN: 152066 Hom.: 1672 Cov.: 34

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.127 AC: 19353 AN: 152184 Hom.: 1676 Cov.: 34 AF XY: 0.130 AC XY: 9654 AN XY: 74398

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.118

Alfa AF: 0.138 Hom.: 692

Bravo AF: 0.128

Asia WGS AF: 0.199 AC: 690 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	0.50
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789964; hg19: chr8-109526728;