chr16-84261750-A-G

Position:

• chr16-84261750-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 0.936 in 152,034 control chromosomes in the GnomAD database, including 66,907 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 0.94 (66907 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 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: 0.936 AC: 142218 AN: 151916 Hom.: 66867 Cov.: 30

Gnomad AFR AF: 0.860

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.936 AC: 142310 AN: 152034 Hom.: 66907 Cov.: 30 AF XY: 0.934 AC XY: 69435 AN XY: 74316

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.972

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.937

Alfa AF: 0.973 Hom.: 3215

Bravo AF: 0.927

Asia WGS AF: 0.824 AC: 2864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.093
DANN	Benign	0.084

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs439927; hg19: chr16-84295356;