16-16143897-A-G

Variant names:

• chr16-16143897-A-G
• rs212093

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 0.484 in 151,772 control chromosomes in the GnomAD database, including 18,216 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 0.48 (18216 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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: 0.484 AC: 73360 AN: 151654 Hom.: 18194 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.484 AC: 73434 AN: 151772 Hom.: 18216 Cov.: 30 AF XY: 0.487 AC XY: 36118 AN XY: 74156

African (AFR) AF: 0.569 AC: 23525 AN: 41358

American (AMR) AF: 0.440 AC: 6702 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1423 AN: 3458

East Asian (EAS) AF: 0.699 AC: 3577 AN: 5120

South Asian (SAS) AF: 0.571 AC: 2745 AN: 4806

European-Finnish (FIN) AF: 0.429 AC: 4512 AN: 10528

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29549 AN: 67940

Other (OTH) AF: 0.476 AC: 1004 AN: 2110

Alfa AF: 0.449 Hom.: 19360

Bravo AF: 0.490

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.096
DANN	Benign	0.29
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs212093; hg19: chr16-16237754;