16-86184620-G-A

Position:

• chr16-86184620-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.545 in 152,052 control chromosomes in the GnomAD database, including 22,927 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (22927 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0220

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 16-86184620-G-A is Benign according to our data. Variant chr16-86184620-G-A is described in ClinVar as [Benign]. Clinvar id is 1597756.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86184620G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82731 AN: 151934 Hom.: 22908 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.545 AC: 82794 AN: 152052 Hom.: 22927 Cov.: 33 AF XY: 0.539 AC XY: 40024 AN XY: 74316

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.528

Alfa AF: 0.585 Hom.: 31871

Bravo AF: 0.530

Asia WGS AF: 0.440 AC: 1531 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4843912; hg19: chr16-86218226;