16-87815297-T-C

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/exons	MANE	UniProt

Ensembl

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