16-52435690-A-T

Variant names:

• chr16-52435690-A-T
• rs7188855

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 0.406 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.406 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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.408

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7188855; hg19: chr16-52469602;