rs276990

Variant names:

• chr16-86187610-A-G
• rs276990

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 0.528 in 151,958 control chromosomes in the GnomAD database, including 24,443 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 0.53 (24443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.528 AC: 80200 AN: 151840 Hom.: 24392 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.528 AC: 80309 AN: 151958 Hom.: 24443 Cov.: 32 AF XY: 0.534 AC XY: 39607 AN XY: 74230

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.531

Alfa AF: 0.402 Hom.: 6344

Bravo AF: 0.560

Asia WGS AF: 0.586 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276990; hg19: chr16-86221216;