16-84954073-C-A

Variant names:

• chr16-84954073-C-A
• rs2326458

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.560 AC: 23189 AN: 41438

American (AMR) AF: 0.594 AC: 9069 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2493 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3570 AN: 5156

South Asian (SAS) AF: 0.602 AC: 2901 AN: 4818

European-Finnish (FIN) AF: 0.792 AC: 8394 AN: 10594

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49787 AN: 67978

Other (OTH) AF: 0.658 AC: 1388 AN: 2108

Alfa AF: 0.707 Hom.: 179315

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs2326458; hg19: chr16-84987679;