16-87078024-A-G

Variant names:

• chr16-87078024-A-G
• rs12933233

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 0.609 in 152,120 control chromosomes in the GnomAD database, including 28,927 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 0.61 (28927 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 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: 0.609 AC: 92633 AN: 152002 Hom.: 28899 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.609 AC: 92717 AN: 152120 Hom.: 28927 Cov.: 33 AF XY: 0.604 AC XY: 44890 AN XY: 74352

African (AFR) AF: 0.505 AC: 20949 AN: 41496

American (AMR) AF: 0.578 AC: 8834 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2355 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1979 AN: 5168

South Asian (SAS) AF: 0.557 AC: 2686 AN: 4822

European-Finnish (FIN) AF: 0.643 AC: 6797 AN: 10570

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47200 AN: 67996

Other (OTH) AF: 0.614 AC: 1298 AN: 2114

Alfa AF: 0.664 Hom.: 120378

Bravo AF: 0.598

Asia WGS AF: 0.476 AC: 1657 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.066
DANN	Benign	0.40
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs12933233; hg19: chr16-87111630;