12-27984936-G-T

Variant names:

• chr12-27984936-G-T
• rs42294

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 0.776 in 152,038 control chromosomes in the GnomAD database, including 45,767 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 0.78 (45767 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.82 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: 0.776 AC: 117850 AN: 151920 Hom.: 45757 Cov.: 30

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.776 AC: 117906 AN: 152038 Hom.: 45767 Cov.: 30 AF XY: 0.781 AC XY: 58079 AN XY: 74320

African (AFR) AF: 0.735 AC: 30452 AN: 41436

American (AMR) AF: 0.832 AC: 12712 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2786 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4001 AN: 5154

South Asian (SAS) AF: 0.822 AC: 3957 AN: 4816

European-Finnish (FIN) AF: 0.840 AC: 8905 AN: 10596

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52539 AN: 67966

Other (OTH) AF: 0.807 AC: 1706 AN: 2114

Alfa AF: 0.783 Hom.: 91703

Bravo AF: 0.772

Asia WGS AF: 0.819 AC: 2845 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.73
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs42294; hg19: chr12-28137869;