16-86183013-C-T

Position:

• chr16-86183013-C-T

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 0.593 in 152,050 control chromosomes in the GnomAD database, including 27,405 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.59 (27405 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.642

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 16-86183013-C-T is Benign according to our data. Variant chr16-86183013-C-T is described in ClinVar as [Benign]. Clinvar id is 1660345.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86183013C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90117 AN: 151932 Hom.: 27383 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.593 AC: 90186 AN: 152050 Hom.: 27405 Cov.: 32 AF XY: 0.586 AC XY: 43549 AN XY: 74344

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.600

Alfa AF: 0.491 Hom.: 1396

Bravo AF: 0.581

Asia WGS AF: 0.463 AC: 1611 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	-0.97
CADD	Benign	0.50
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11641863; hg19: chr16-86216619;