16-587212-T-C

Variant names:

• chr16-587212-T-C
• rs2017567

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 0.463 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.414

Alfa AF: 0.422 Hom.: 6180

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2017567; hg19: chr16-637212;