rs3923693

Variant names:

• chr12-47943846-C-T
• rs3923693

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 0.167 in 152,300 control chromosomes in the GnomAD database, including 2,555 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 (2555 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.167 AC: 25366 AN: 152182 Hom.: 2540 Cov.: 34

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.167 AC: 25411 AN: 152300 Hom.: 2555 Cov.: 34 AF XY: 0.171 AC XY: 12707 AN XY: 74458

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.161

Alfa AF: 0.132 Hom.: 304

Bravo AF: 0.182

Asia WGS AF: 0.233 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	10
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3923693; hg19: chr12-48337629;