rs276992

Variant names:

• chr16-86187097-C-G
• rs276992

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 0.518 in 152,112 control chromosomes in the GnomAD database, including 23,304 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 0.52 (23304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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: 0.517 AC: 78649 AN: 151994 Hom.: 23261 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.518 AC: 78747 AN: 152112 Hom.: 23304 Cov.: 32 AF XY: 0.523 AC XY: 38915 AN XY: 74350

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.520

Alfa AF: 0.452 Hom.: 2194

Bravo AF: 0.547

Asia WGS AF: 0.584 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276992; hg19: chr16-86220703;