rs12596316

Variant names:

• chr16-82612547-A-G
• rs12596316

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 0.383 in 152,050 control chromosomes in the GnomAD database, including 11,952 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 0.38 (11952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.383 AC: 58180 AN: 151932 Hom.: 11951 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.383 AC: 58192 AN: 152050 Hom.: 11952 Cov.: 33 AF XY: 0.387 AC XY: 28797 AN XY: 74324

African (AFR) AF: 0.248 AC: 10287 AN: 41454

American (AMR) AF: 0.309 AC: 4719 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1477 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1751 AN: 5160

South Asian (SAS) AF: 0.431 AC: 2078 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5832 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30660 AN: 67972

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.396 Hom.: 2447

Bravo AF: 0.354

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.59
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs12596316; hg19: chr16-82646152;