16-87870525-A-G

Variant names:

• chr16-87870525-A-G
• rs4356486

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 0.317 in 151,972 control chromosomes in the GnomAD database, including 7,861 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 0.32 (7861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.317 AC: 48074 AN: 151854 Hom.: 7851 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.317 AC: 48124 AN: 151972 Hom.: 7861 Cov.: 32 AF XY: 0.313 AC XY: 23243 AN XY: 74284

African (AFR) AF: 0.358 AC: 14822 AN: 41456

American (AMR) AF: 0.235 AC: 3587 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3468

East Asian (EAS) AF: 0.146 AC: 744 AN: 5102

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4812

European-Finnish (FIN) AF: 0.270 AC: 2863 AN: 10594

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22442 AN: 67946

Other (OTH) AF: 0.308 AC: 649 AN: 2110

Alfa AF: 0.184 Hom.: 381

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.8
DANN	Benign	0.40
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs4356486; hg19: chr16-87904131;