rs1991867

chr16-82485623-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;