chr16-52714430-C-T

Variant names:

• chr16-52714430-C-T
• rs1420247

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 0.788 in 151,928 control chromosomes in the GnomAD database, including 47,541 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 0.79 (47541 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.788 AC: 119576 AN: 151810 Hom.: 47505 Cov.: 29

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.788 AC: 119660 AN: 151928 Hom.: 47541 Cov.: 29 AF XY: 0.787 AC XY: 58385 AN XY: 74196

African (AFR) AF: 0.883 AC: 36596 AN: 41466

American (AMR) AF: 0.806 AC: 12299 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2549 AN: 3464

East Asian (EAS) AF: 0.886 AC: 4570 AN: 5160

South Asian (SAS) AF: 0.764 AC: 3650 AN: 4778

European-Finnish (FIN) AF: 0.727 AC: 7648 AN: 10524

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49800 AN: 67966

Other (OTH) AF: 0.749 AC: 1572 AN: 2098

Alfa AF: 0.749 Hom.: 5289

Bravo AF: 0.799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.96
DANN	Benign	0.80
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs1420247; hg19: chr16-52748342;