rs12596316

Positions:

• chr16-82612547-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.376

Alfa AF: 0.400 Hom.: 2425

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12596316; hg19: chr16-82646152;