16-85954392-A-G

Position:

• chr16-85954392-A-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 0.639 in 152,208 control chromosomes in the GnomAD database, including 32,283 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 0.64 (32283 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.639 AC: 97198 AN: 152092 Hom.: 32269 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.639 AC: 97246 AN: 152208 Hom.: 32283 Cov.: 33 AF XY: 0.648 AC XY: 48201 AN XY: 74430

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.618

Alfa AF: 0.671 Hom.: 5889

Bravo AF: 0.620

Asia WGS AF: 0.734 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10863202; hg19: chr16-85987998;