16-86509420-C-G

Position:

• chr16-86509420-C-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 0.683 in 152,236 control chromosomes in the GnomAD database, including 36,747 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 0.68 (36747 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103897 AN: 152118 Hom.: 36720 Cov.: 36

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.683 AC: 103978 AN: 152236 Hom.: 36747 Cov.: 36 AF XY: 0.688 AC XY: 51190 AN XY: 74438

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.718

Alfa AF: 0.704 Hom.: 4759

Bravo AF: 0.680

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364225; hg19: chr16-86543026;