16-84240799-T-G

Variant names:

• chr16-84240799-T-G
• rs746080

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;