16-52435690-A-T

Variant names:

• chr16-52435690-A-T
• rs7188855

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 0.406 in 151,976 control chromosomes in the GnomAD database, including 12,838 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 0.41 (12838 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 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: 0.406 AC: 61640 AN: 151856 Hom.: 12822 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.406 AC: 61674 AN: 151976 Hom.: 12838 Cov.: 31 AF XY: 0.403 AC XY: 29941 AN XY: 74256

African (AFR) AF: 0.343 AC: 14222 AN: 41424

American (AMR) AF: 0.343 AC: 5244 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1547 AN: 5172

South Asian (SAS) AF: 0.413 AC: 1993 AN: 4826

European-Finnish (FIN) AF: 0.477 AC: 5030 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30480 AN: 67948

Other (OTH) AF: 0.408 AC: 860 AN: 2106

Alfa AF: 0.441 Hom.: 1893

Bravo AF: 0.393

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	4.3
DANN	Benign	0.77
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs7188855; hg19: chr16-52469602;