12-87591363-A-C

Variant names:

• chr12-87591363-A-C
• rs790419

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 0.258 in 149,980 control chromosomes in the GnomAD database, including 5,182 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 0.26 (5182 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 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: 0.258 AC: 38625 AN: 149866 Hom.: 5159 Cov.: 30

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.258 AC: 38691 AN: 149980 Hom.: 5182 Cov.: 30 AF XY: 0.260 AC XY: 19025 AN XY: 73194

African (AFR) AF: 0.314 AC: 12664 AN: 40304

American (AMR) AF: 0.275 AC: 4146 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 856 AN: 3452

East Asian (EAS) AF: 0.325 AC: 1639 AN: 5038

South Asian (SAS) AF: 0.328 AC: 1556 AN: 4748

European-Finnish (FIN) AF: 0.224 AC: 2344 AN: 10460

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14764 AN: 67630

Other (OTH) AF: 0.226 AC: 468 AN: 2074

Alfa AF: 0.123 Hom.: 202

Bravo AF: 0.268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs790419; hg19: chr12-87985140;