rs12682293

Variant names:

• chr8-30026561-A-C
• rs12682293

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 0.416 in 152,136 control chromosomes in the GnomAD database, including 16,222 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 0.42 (16222 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63320 AN: 152016 Hom.: 16223 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.416 AC: 63325 AN: 152136 Hom.: 16222 Cov.: 33 AF XY: 0.414 AC XY: 30821 AN XY: 74374

African (AFR) AF: 0.125 AC: 5197 AN: 41534

American (AMR) AF: 0.505 AC: 7716 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1026 AN: 5176

South Asian (SAS) AF: 0.382 AC: 1837 AN: 4814

European-Finnish (FIN) AF: 0.554 AC: 5849 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38154 AN: 67984

Other (OTH) AF: 0.434 AC: 917 AN: 2114

Alfa AF: 0.510 Hom.: 9225

Bravo AF: 0.402

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.5
DANN	Benign	0.88
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs12682293; hg19: chr8-29884077;