chr12-58819362-A-G

Variant names:

• chr12-58819362-A-G
• rs6581219

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 0.429 in 152,110 control chromosomes in the GnomAD database, including 14,098 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 0.43 (14098 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 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: 0.429 AC: 65241 AN: 151992 Hom.: 14084 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.429 AC: 65287 AN: 152110 Hom.: 14098 Cov.: 33 AF XY: 0.431 AC XY: 32041 AN XY: 74348

African (AFR) AF: 0.427 AC: 17736 AN: 41488

American (AMR) AF: 0.491 AC: 7514 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3464

East Asian (EAS) AF: 0.418 AC: 2155 AN: 5156

South Asian (SAS) AF: 0.447 AC: 2159 AN: 4828

European-Finnish (FIN) AF: 0.408 AC: 4313 AN: 10574

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28730 AN: 67984

Other (OTH) AF: 0.422 AC: 891 AN: 2110

Alfa AF: 0.427 Hom.: 2350

Bravo AF: 0.434

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.23
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6581219; hg19: chr12-59213144;