16-82485623-C-T

Variant names:

• chr16-82485623-C-T
• rs1991867

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 0.82 in 151,946 control chromosomes in the GnomAD database, including 51,747 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 0.82 (51747 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124538 AN: 151828 Hom.: 51742 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.820 AC: 124581 AN: 151946 Hom.: 51747 Cov.: 31 AF XY: 0.821 AC XY: 61004 AN XY: 74272

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.838

Alfa AF: 0.883 Hom.: 89971

Bravo AF: 0.802

Asia WGS AF: 0.794 AC: 2753 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991867; hg19: chr16-82519228;