16-84954073-C-A

Position:

• chr16-84954073-C-A

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 0.669 in 152,044 control chromosomes in the GnomAD database, including 34,535 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 0.67 (34535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 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: 0.669 AC: 101635 AN: 151924 Hom.: 34528 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.669 AC: 101686 AN: 152044 Hom.: 34535 Cov.: 32 AF XY: 0.669 AC XY: 49711 AN XY: 74314

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.658

Alfa AF: 0.715 Hom.: 88276

Bravo AF: 0.653

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2326458; hg19: chr16-84987679;