rs3829787

Variant names:

• chr15-78563924-C-T
• rs3829787

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 0.27 in 152,182 control chromosomes in the GnomAD database, including 6,446 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 0.27 (6446 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.271 AC: 41165 AN: 152064 Hom.: 6449 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.270 AC: 41155 AN: 152182 Hom.: 6446 Cov.: 33 AF XY: 0.268 AC XY: 19940 AN XY: 74394

African (AFR) AF: 0.125 AC: 5202 AN: 41544

American (AMR) AF: 0.206 AC: 3150 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3470

East Asian (EAS) AF: 0.166 AC: 859 AN: 5180

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3568 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25001 AN: 67972

Other (OTH) AF: 0.271 AC: 574 AN: 2116

Alfa AF: 0.246 Hom.: 1325

Bravo AF: 0.255

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.51
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs3829787; hg19: chr15-78856266;