16-87815297-T-C

Variant names:

• chr16-87815297-T-C
• rs9921866

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 0.655 in 152,112 control chromosomes in the GnomAD database, including 33,923 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 0.65 (33923 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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: 0.655 AC: 99497 AN: 151994 Hom.: 33881 Cov.: 33

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.655 AC: 99587 AN: 152112 Hom.: 33923 Cov.: 33 AF XY: 0.665 AC XY: 49424 AN XY: 74358

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.616

Alfa AF: 0.562 Hom.: 46491

Bravo AF: 0.666

Asia WGS AF: 0.869 AC: 3020 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	1.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9921866; hg19: chr16-87848903;