rs3862406

Variant names:

• chr12-33718488-G-A
• rs3862406

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 0.277 in 152,020 control chromosomes in the GnomAD database, including 7,127 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 (7127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

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 (NFE) allele frequency at 95% confidence interval = 0.361 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: 0.277 AC: 42028 AN: 151902 Hom.: 7126 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.277 AC: 42035 AN: 152020 Hom.: 7127 Cov.: 32 AF XY: 0.278 AC XY: 20643 AN XY: 74274

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0648

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.281

Alfa AF: 0.300 Hom.: 1004

Bravo AF: 0.266

Asia WGS AF: 0.147 AC: 512 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	0.86
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3862406; hg19: chr12-33871423;