16-587212-T-C

Variant names:

• chr16-587212-T-C
• rs2017567

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.463 in 152,032 control chromosomes in the GnomAD database, including 16,693 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 0.46 (16693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 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: 0.462 AC: 70254 AN: 151914 Hom.: 16663 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.463 AC: 70339 AN: 152032 Hom.: 16693 Cov.: 32 AF XY: 0.471 AC XY: 34995 AN XY: 74314

African (AFR) AF: 0.488 AC: 20232 AN: 41476

American (AMR) AF: 0.482 AC: 7368 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3306 AN: 5156

South Asian (SAS) AF: 0.633 AC: 3055 AN: 4824

European-Finnish (FIN) AF: 0.506 AC: 5365 AN: 10600

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28376 AN: 67918

Other (OTH) AF: 0.414 AC: 875 AN: 2114

Alfa AF: 0.436 Hom.: 26120

Bravo AF: 0.455

Asia WGS AF: 0.660 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2017567; hg19: chr16-637212;