16-51096222-A-G

Position:

• chr16-51096222-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 0.116 in 152,158 control chromosomes in the GnomAD database, including 2,317 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 0.12 (2317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.116 AC: 17659 AN: 152040 Hom.: 2318 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.116 AC: 17666 AN: 152158 Hom.: 2317 Cov.: 32 AF XY: 0.114 AC XY: 8461 AN XY: 74412

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0368

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0460 Hom.: 526

Bravo AF: 0.127

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7195127; hg19: chr16-51130133;