rs1384769

Variant names:

• chr8-93072108-G-A
• rs1384769

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 0.174 in 151,868 control chromosomes in the GnomAD database, including 3,215 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 (3215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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: 0.173 AC: 26325 AN: 151750 Hom.: 3204 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.174 AC: 26375 AN: 151868 Hom.: 3215 Cov.: 32 AF XY: 0.174 AC XY: 12907 AN XY: 74236

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0558

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.176

Alfa AF: 0.107 Hom.: 684

Bravo AF: 0.190

Asia WGS AF: 0.270 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1384769; hg19: chr8-94084336; COSMIC: COSV57968839;