16-55357720-A-T

Variant names:

• chr16-55357720-A-T
• rs365760

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 0.381 in 152,000 control chromosomes in the GnomAD database, including 12,382 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 0.38 (12382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57836 AN: 151882 Hom.: 12348 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.381 AC: 57918 AN: 152000 Hom.: 12382 Cov.: 32 AF XY: 0.381 AC XY: 28287 AN XY: 74274

African (AFR) AF: 0.584 AC: 24221 AN: 41444

American (AMR) AF: 0.388 AC: 5929 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1957 AN: 5164

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4816

European-Finnish (FIN) AF: 0.299 AC: 3165 AN: 10572

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19626 AN: 67960

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.359 Hom.: 1288

Bravo AF: 0.395

Asia WGS AF: 0.337 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs365760; hg19: chr16-55391632;