12-128048327-C-G

Variant names:

• chr12-128048327-C-G
• rs6489226

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 0.609 in 152,102 control chromosomes in the GnomAD database, including 30,457 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 0.61 (30457 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 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: 0.609 AC: 92555 AN: 151984 Hom.: 30396 Cov.: 33

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.609 AC: 92686 AN: 152102 Hom.: 30457 Cov.: 33 AF XY: 0.610 AC XY: 45330 AN XY: 74338

African (AFR) AF: 0.865 AC: 35923 AN: 41542

American (AMR) AF: 0.661 AC: 10100 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2766 AN: 5152

South Asian (SAS) AF: 0.517 AC: 2493 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5074 AN: 10554

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32701 AN: 67972

Other (OTH) AF: 0.608 AC: 1280 AN: 2106

Alfa AF: 0.549 Hom.: 3013

Bravo AF: 0.636

Asia WGS AF: 0.574 AC: 1999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.53
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6489226; hg19: chr12-128532872; COSMIC: COSV107182583;