16-84240799-T-G

Position:

• chr16-84240799-T-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 0.742 in 152,020 control chromosomes in the GnomAD database, including 42,013 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 0.74 (42013 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.742 AC: 112641 AN: 151902 Hom.: 41968 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.742 AC: 112745 AN: 152020 Hom.: 42013 Cov.: 31 AF XY: 0.749 AC XY: 55600 AN XY: 74262

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.765

Alfa AF: 0.717 Hom.: 81912

Bravo AF: 0.749

Asia WGS AF: 0.867 AC: 3014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs746080; hg19: chr16-84274405;