rs1786330

Variant names:

• chr8-100679902-C-T
• rs1786330

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 0.284 in 151,934 control chromosomes in the GnomAD database, including 6,238 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 0.28 (6238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 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: 0.284 AC: 43094 AN: 151814 Hom.: 6237 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.284 AC: 43096 AN: 151934 Hom.: 6238 Cov.: 31 AF XY: 0.285 AC XY: 21159 AN XY: 74238

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.278

Alfa AF: 0.310 Hom.: 1374

Bravo AF: 0.269

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1786330; hg19: chr8-101692130; COSMIC: COSV72762458;