12-49950079-A-G

Variant names:

• chr12-49950079-A-G
• rs3759126

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 0.228 in 152,160 control chromosomes in the GnomAD database, including 4,165 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 0.23 (4165 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34680 AN: 152040 Hom.: 4167 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.228 AC: 34690 AN: 152160 Hom.: 4165 Cov.: 33 AF XY: 0.230 AC XY: 17120 AN XY: 74394

African (AFR) AF: 0.260 AC: 10778 AN: 41494

American (AMR) AF: 0.175 AC: 2684 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2043 AN: 5156

South Asian (SAS) AF: 0.335 AC: 1617 AN: 4830

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10594

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13685 AN: 68004

Other (OTH) AF: 0.245 AC: 517 AN: 2106

Alfa AF: 0.211 Hom.: 4891

Bravo AF: 0.226

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs3759126; hg19: chr12-50343862;