16-86674163-G-A

Position:

• chr16-86674163-G-A

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 0.207 in 131,306 control chromosomes in the GnomAD database, including 2,643 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 0.21 (2643 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.207 AC: 27162 AN: 131162 Hom.: 2639 Cov.: 26

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.207 AC: 27190 AN: 131306 Hom.: 2643 Cov.: 26 AF XY: 0.207 AC XY: 13177 AN XY: 63518

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.189

Alfa AF: 0.164 Hom.: 778

Bravo AF: 0.180

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7188801; hg19: chr16-86707769;