16-52894214-T-G

Variant names:

• chr16-52894214-T-G
• rs1362441

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 0.523 in 152,052 control chromosomes in the GnomAD database, including 21,373 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 0.52 (21373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79466 AN: 151934 Hom.: 21357 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.523 AC: 79518 AN: 152052 Hom.: 21373 Cov.: 32 AF XY: 0.526 AC XY: 39071 AN XY: 74314

African (AFR) AF: 0.416 AC: 17251 AN: 41474

American (AMR) AF: 0.652 AC: 9947 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3858 AN: 5182

South Asian (SAS) AF: 0.505 AC: 2430 AN: 4812

European-Finnish (FIN) AF: 0.567 AC: 5995 AN: 10580

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37026 AN: 67956

Other (OTH) AF: 0.522 AC: 1103 AN: 2112

Alfa AF: 0.557 Hom.: 4177

Bravo AF: 0.528

Asia WGS AF: 0.589 AC: 2048 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1362441; hg19: chr16-52928126;