rs3847859

Variant names:

• chr12-51899716-G-A
• rs3847859

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 0.394 in 152,064 control chromosomes in the GnomAD database, including 12,045 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 0.39 (12045 hom., cov: 32)
• Consequence: LOC102724178 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 8 publications found

Genes affected

LOC102724178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 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: 0.394 AC: 59858 AN: 151946 Hom.: 12040 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.394 AC: 59896 AN: 152064 Hom.: 12045 Cov.: 32 AF XY: 0.395 AC XY: 29393 AN XY: 74328

African (AFR) AF: 0.430 AC: 17836 AN: 41460

American (AMR) AF: 0.316 AC: 4832 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1804 AN: 5166

South Asian (SAS) AF: 0.430 AC: 2070 AN: 4814

European-Finnish (FIN) AF: 0.416 AC: 4399 AN: 10572

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26333 AN: 67984

Other (OTH) AF: 0.400 AC: 844 AN: 2108

Alfa AF: 0.384 Hom.: 50667

Bravo AF: 0.386

Asia WGS AF: 0.386 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs3847859; hg19: chr12-52293500;