rs12927327

Variant names:

• chr16-78081611-C-T
• rs12927327

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 0.227 in 152,016 control chromosomes in the GnomAD database, including 4,814 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 0.23 (4814 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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: 0.227 AC: 34516 AN: 151898 Hom.: 4811 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.227 AC: 34508 AN: 152016 Hom.: 4814 Cov.: 32 AF XY: 0.229 AC XY: 17014 AN XY: 74292

African (AFR) AF: 0.0570 AC: 2366 AN: 41494

American (AMR) AF: 0.222 AC: 3391 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1069 AN: 5148

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4802

European-Finnish (FIN) AF: 0.379 AC: 3995 AN: 10552

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20750 AN: 67966

Other (OTH) AF: 0.214 AC: 451 AN: 2104

Alfa AF: 0.258 Hom.: 776

Bravo AF: 0.209

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.64
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12927327; hg19: chr16-78115508;