chr16-87870525-A-G

Position:

• chr16-87870525-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.308

Alfa AF: 0.0996 Hom.: 129

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4356486; hg19: chr16-87904131;