16-87870563-A-G

Variant names:

• chr16-87870563-A-G
• rs8055157

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 0.182 in 151,908 control chromosomes in the GnomAD database, including 2,743 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 0.18 (2743 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27672 AN: 151786 Hom.: 2739 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.182 AC: 27690 AN: 151908 Hom.: 2743 Cov.: 33 AF XY: 0.181 AC XY: 13434 AN XY: 74260

African (AFR) AF: 0.131 AC: 5444 AN: 41446

American (AMR) AF: 0.152 AC: 2323 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3472

East Asian (EAS) AF: 0.142 AC: 714 AN: 5024

South Asian (SAS) AF: 0.266 AC: 1278 AN: 4810

European-Finnish (FIN) AF: 0.154 AC: 1632 AN: 10592

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14675 AN: 67958

Other (OTH) AF: 0.199 AC: 420 AN: 2106

Alfa AF: 0.171 Hom.: 848

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.89
DANN	Benign	0.42
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs8055157; hg19: chr16-87904169;