12-84572395-A-C

Variant names:

• chr12-84572395-A-C
• rs7967594

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 0.533 in 151,858 control chromosomes in the GnomAD database, including 22,686 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 0.53 (22686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.748 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: 0.533 AC: 80925 AN: 151740 Hom.: 22684 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.533 AC: 80966 AN: 151858 Hom.: 22686 Cov.: 31 AF XY: 0.537 AC XY: 39881 AN XY: 74232

African (AFR) AF: 0.384 AC: 15876 AN: 41390

American (AMR) AF: 0.500 AC: 7633 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1601 AN: 3466

East Asian (EAS) AF: 0.768 AC: 3947 AN: 5136

South Asian (SAS) AF: 0.432 AC: 2081 AN: 4816

European-Finnish (FIN) AF: 0.703 AC: 7413 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40660 AN: 67926

Other (OTH) AF: 0.509 AC: 1072 AN: 2108

Alfa AF: 0.560 Hom.: 77859

Bravo AF: 0.512

Asia WGS AF: 0.579 AC: 2012 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	0.91
DANN	Benign	0.51
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7967594; hg19: chr12-84966174;