16-86096925-T-C

Position:

• chr16-86096925-T-C

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 0.0905 in 152,228 control chromosomes in the GnomAD database, including 1,015 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 0.091 (1015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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: 0.0904 AC: 13757 AN: 152110 Hom.: 1007 Cov.: 33

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0905 AC: 13781 AN: 152228 Hom.: 1015 Cov.: 33 AF XY: 0.0964 AC XY: 7172 AN XY: 74410

Gnomad4 AFR AF: 0.0748

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.0556

Gnomad4 OTH AF: 0.0718

Alfa AF: 0.0768 Hom.: 404

Bravo AF: 0.103

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514613; hg19: chr16-86130531;