rs1789964

Variant names:

• chr8-108514499-G-A
• rs1789964

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;