12-48972367-C-G

Variant names:

• chr12-48972367-C-G
• rs833840

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 0.369 in 151,880 control chromosomes in the GnomAD database, including 11,768 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 0.37 (11768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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: 0.369 AC: 56063 AN: 151760 Hom.: 11773 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.369 AC: 56055 AN: 151880 Hom.: 11768 Cov.: 31 AF XY: 0.371 AC XY: 27512 AN XY: 74204

African (AFR) AF: 0.161 AC: 6681 AN: 41464

American (AMR) AF: 0.342 AC: 5227 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3464

East Asian (EAS) AF: 0.533 AC: 2720 AN: 5102

South Asian (SAS) AF: 0.501 AC: 2413 AN: 4818

European-Finnish (FIN) AF: 0.472 AC: 4981 AN: 10544

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31274 AN: 67910

Other (OTH) AF: 0.362 AC: 762 AN: 2106

Alfa AF: 0.408 Hom.: 1722

Bravo AF: 0.347

Asia WGS AF: 0.467 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs833840; hg19: chr12-49366150;