16-86384470-C-T

Variant names:

• chr16-86384470-C-T
• rs4843368

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 0.346 in 152,014 control chromosomes in the GnomAD database, including 9,184 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 0.35 (9184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52523 AN: 151896 Hom.: 9181 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.346 AC: 52567 AN: 152014 Hom.: 9184 Cov.: 32 AF XY: 0.346 AC XY: 25706 AN XY: 74296

African (AFR) AF: 0.342 AC: 14200 AN: 41468

American (AMR) AF: 0.407 AC: 6226 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3464

East Asian (EAS) AF: 0.502 AC: 2584 AN: 5150

South Asian (SAS) AF: 0.382 AC: 1831 AN: 4796

European-Finnish (FIN) AF: 0.306 AC: 3229 AN: 10568

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21873 AN: 67962

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.316 Hom.: 5376

Bravo AF: 0.351

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.26
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4843368; hg19: chr16-86418076;