12-48961253-G-A

Variant names:

• chr12-48961253-G-A
• rs4018511

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 0.0825 in 152,274 control chromosomes in the GnomAD database, including 978 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 0.082 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12527 AN: 152156 Hom.: 966 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0825 AC: 12555 AN: 152274 Hom.: 978 Cov.: 32 AF XY: 0.0880 AC XY: 6554 AN XY: 74448

African (AFR) AF: 0.0186 AC: 775 AN: 41566

American (AMR) AF: 0.227 AC: 3476 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0426 AC: 148 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1383 AN: 5180

South Asian (SAS) AF: 0.0817 AC: 395 AN: 4832

European-Finnish (FIN) AF: 0.125 AC: 1329 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4824 AN: 68024

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0818 Hom.: 1497

Bravo AF: 0.0919

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4018511; hg19: chr12-49355036;