16-16902859-A-G

Position:

• chr16-16902859-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 0.0556 in 152,192 control chromosomes in the GnomAD database, including 289 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 0.056 (289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8466 AN: 152074 Hom.: 289 Cov.: 31

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0556 AC: 8463 AN: 152192 Hom.: 289 Cov.: 31 AF XY: 0.0559 AC XY: 4161 AN XY: 74402

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0632

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.0510

Alfa AF: 0.0553 Hom.: 35

Bravo AF: 0.0525

Asia WGS AF: 0.119 AC: 411 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12926231; hg19: chr16-16996716;