chr12-84597422-C-T

Variant names:

• chr12-84597422-C-T
• rs1380412

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 0.628 in 152,018 control chromosomes in the GnomAD database, including 30,443 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 0.63 (30443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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: 0.628 AC: 95355 AN: 151900 Hom.: 30419 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.628 AC: 95434 AN: 152018 Hom.: 30443 Cov.: 32 AF XY: 0.629 AC XY: 46749 AN XY: 74278

African (AFR) AF: 0.688 AC: 28527 AN: 41460

American (AMR) AF: 0.544 AC: 8297 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1630 AN: 3462

East Asian (EAS) AF: 0.804 AC: 4150 AN: 5160

South Asian (SAS) AF: 0.484 AC: 2330 AN: 4818

European-Finnish (FIN) AF: 0.706 AC: 7458 AN: 10566

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41150 AN: 67988

Other (OTH) AF: 0.573 AC: 1209 AN: 2110

Alfa AF: 0.603 Hom.: 14302

Bravo AF: 0.619

Asia WGS AF: 0.641 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.62
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1380412; hg19: chr12-84991201;