rs3923693

Variant names:

• chr12-47943846-C-T
• rs3923693

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 0.167 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.167 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

African (AFR) AF: 0.203 AC: 8417 AN: 41554

American (AMR) AF: 0.289 AC: 4418 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1631 AN: 5182

South Asian (SAS) AF: 0.145 AC: 698 AN: 4826

European-Finnish (FIN) AF: 0.149 AC: 1582 AN: 10616

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7716 AN: 68028

Other (OTH) AF: 0.161 AC: 341 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs3923693; hg19: chr12-48337629;