16-86430089-T-C

Variant names:

• chr16-86430089-T-C
• rs2178146

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 0.308 in 152,062 control chromosomes in the GnomAD database, including 9,079 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 0.31 (9079 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 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: 0.308 AC: 46792 AN: 151944 Hom.: 9074 Cov.: 31

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.308 AC: 46803 AN: 152062 Hom.: 9079 Cov.: 31 AF XY: 0.316 AC XY: 23512 AN XY: 74318

African (AFR) AF: 0.0738 AC: 3062 AN: 41518

American (AMR) AF: 0.388 AC: 5931 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1161 AN: 5142

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4812

European-Finnish (FIN) AF: 0.558 AC: 5898 AN: 10576

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27466 AN: 67956

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.358 Hom.: 19406

Bravo AF: 0.283

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2178146; hg19: chr16-86463695;