rs1789964

Variant names:

• chr8-108514499-G-A
• rs1789964

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0309 AC: 1281 AN: 41520

American (AMR) AF: 0.217 AC: 3326 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1805 AN: 5172

South Asian (SAS) AF: 0.114 AC: 549 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1618 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9989 AN: 68002

Other (OTH) AF: 0.118 AC: 249 AN: 2106

Alfa AF: 0.138 Hom.: 768

Bravo AF: 0.128

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.82
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1789964; hg19: chr8-109526728;