chr16-750821-A-G

Position:

• chr16-750821-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 0.28 in 152,170 control chromosomes in the GnomAD database, including 6,758 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 0.28 (6758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 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: 0.280 AC: 42618 AN: 152052 Hom.: 6766 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.280 AC: 42608 AN: 152170 Hom.: 6758 Cov.: 33 AF XY: 0.278 AC XY: 20706 AN XY: 74378

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.282

Alfa AF: 0.334 Hom.: 12992

Bravo AF: 0.267

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12102635; hg19: chr16-800821;